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Urbana, IL, United States

The University of Illinois at Urbana–Champaign is a public research-intensive university in the U.S. state of Illinois. A land-grant university, it is the flagship campus of the University of Illinois system. The University of Illinois at Urbana–Champaign is the second oldest public university in the state , and is a founding member of the Big Ten Conference. It is a member of the Association of American Universities and is designated as a RU/VH Research University . The campus library system possesses the second-largest university library in the United States after Harvard University.The university comprises 17 colleges that offer more than 150 programs of study. Additionally, the university operates an extension that serves 2.7 million registrants per year around the state of Illinois and beyond. The campus holds 647 buildings on 4,552 acres in the twin cities of Champaign and Urbana ; its annual operating budget in 2011 was over $1.7 billion. Wikipedia.


Olshevsky A.,University of Illinois at Urbana - Champaign
IEEE Transactions on Control of Network Systems | Year: 2014

Given a linear system, we consider the problem of finding a small set of variables to affect with an input so that the resulting system is controllable. We show that this problem is NP-hard; indeed, we show that even approximating the minimum number of variables that need to be affected within a multiplicative factor of clog n is NP-hard for some positive c. On the positive side, we show it is possible to find sets of variables matching this in approximability barrier in polynomial time. This can be done with a simple greedy heuristic which sequentially picks variables to maximize the rank increase of the controllability matrix. Experiments on Erdos-Renyi random graphs that demonstrate this heuristic almost always succeed at finding the minimum number of variables. © 2014 IEEE.


Zhang K.,University of Illinois at Urbana - Champaign | Cui B.,Stanford University
Trends in Biotechnology | Year: 2015

Cells employ a plethora of signaling pathways to make their life-and-death decisions. Extensive genetic, biochemical, and physiological studies have led to the accumulation of knowledge about signaling components and their interactions within signaling networks. These conventional approaches, although useful, lack the ability to control the spatial and temporal aspects of signaling processes. The recently emerged optogenetic tools open exciting opportunities by enabling signaling regulation with superior temporal and spatial resolution, easy delivery, rapid reversibility, fewer off-target side effects, and the ability to dissect complex signaling networks. Here we review recent achievements in using light to control intracellular signaling pathways and discuss future prospects for the field, including integration of new genetic approaches into optogenetics. © 2014 Elsevier Ltd.


Miller G.A.,University of Delaware | Miller G.A.,University of Konstanz | Miller G.A.,University of Illinois at Urbana - Champaign | Rockstroh B.,University of Konstanz
Annual Review of Clinical Psychology | Year: 2013

Endophenotypes for psychopathology have been conceived as latent, unobserved, but measureable manifestations of phenomena that causally connect genetic liability to clinical disorder. Several decades of research have led to refinement of the construct and identification of some candidate endophenotypes, but rather limited progress on finding the genes involved or the mechanisms by which endophenotypes are driven by genetic and environmental factors and in turn drive psychopathology. Currently promising avenues for research involve development of transdiagnostic concepts not limited to traditional diagnostic categories, measures of endophenotypic and manifest psychopathology that have higher validity than those categories, and methods for modeling complex relationships among diverse contributors to etiology. With more grounding in animal neuroscience and other aspects of basic biological and psychological science, exemplified in the Research Domain Criteria initiative, there is every reason to anticipate that the endophenotype concept will grow more central in the psychopathology literature. Copyright © 2013 by Annual Reviews.


Zhou E.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2013

We propose a new approximate value iteration method, namely near-value iteration (NVI), to solve continuous-state optimal stopping problems under partial observation, which in general cannot be solved analytically and also pose a great challenge to numerical solutions. NVI is motivated by the expression of the value function as the supremum over an uncountable set of linear functions in the belief state. After a smart manipulation of the operations in the updating equation for the value function, we reduce the set to only two functions at every time step, so as to achieve significant computational savings. NVI yields a value function approximation bounded by the tightest lower and upper bounds that can be achieved by existing algorithms in the same class, so the NVI approximation is closer to the true value function than at least one of these bounds. We demonstrate the effectiveness of our approach on an example of pricing American options under stochastic volatility. © 2012 IEEE.


Zong X.,University of Illinois at Urbana - Champaign
RNA biology | Year: 2011

The mammalian genome harbors a large number of long non-coding RNAs (lncRNAs) that do not code for proteins, but rather they exert their function directly as RNA molecules. LncRNAs are involved in executing several vital cellular functions. They facilitate the recruitment of proteins to specific chromatin sites, ultimately regulating processes like dosage compensation and genome imprinting. LncRNAs are also known to regulate nucleocytoplasmic transport of macromolecules. A large number of the regulatory lncRNAs are retained within the cell nucleus and constitute a subclass termed nuclear-retained RNAs (nrRNAs). NrRNAs are speculated to be involved in crucial gene regulatory networks, acting as structural scaffolds of subnuclear domains. NrRNAs modulate gene expression by influencing chromatin modification, transcription and post-transcriptional gene processing. The cancer-associated Metastasis-associated lung adenocarcinoma transcript1 (MALAT1) is one such long nrRNA that regulates pre-mRNA processing in mammalian cells. Thus far, our understanding about the roles played by nrRNAs and their relevance in disease pathways is only 'a tip of an iceberg'. It will therefore be crucial to unravel the functions for the vast number of long nrRNAs, buried within the complex mine of the human genome.


Bretl T.,University of Illinois at Urbana - Champaign
IEEE Transactions on Robotics | Year: 2012

In this paper, we solve the minimum-time optimal control problem for a group of robots that can move at different speeds but that must all move in the same direction. We are motivated to solve this problem because constraints of this sort are common in micro-scale and nano-scale robotic systems. By application of the minimum principle, we obtain necessary conditions for optimality and use them to guess a candidate control policy. By showing that the corresponding value function is a viscosity solution to the Hamilton-Jacobi-Bellman equation, we verify that our guess is optimal. The complexity of finding this policy for arbitrary initial conditions is only quasilinear in the number of robots, and in fact is dominated by the computation of a planar convex hull. We extend this result to consider obstacle avoidance by explicit parameterization of all possible optimal control policies, and show examples in simulation. © 2012 IEEE.


Wypij J.M.,University of Illinois at Urbana - Champaign
Pathology Research International | Year: 2013

Despite advances in understanding cancer at the molecular level, timely and effective translation to clinical application of novel therapeutics in human cancer patients is lacking. Cancer drug failure is often a result of toxicity or inefficacy not predicted by preclinical models, emphasizing the need for alternative animal tumor models with improved biologic relevancy. Companion animals (dogs and cats) provide an opportunity to capitalize on an underutilized and biologically relevant translational research model which allows spontaneous disease modeling of human cancer. Head and neck squamous cell carcinoma (HNSCC) is a common cancer with a poor prognosis and limited clinical advancements in recent years. One potential novel spontaneous animal tumor model is feline oral squamous cell carcinoma (FOSCC). FOSCC and HNSCC share similar etiopathogenesis (tobacco and papillomavirus exposure) and molecular markers (EGFR, VEGF, and p53). Both human and feline SCCs share similar tumor biology, clinical outcome, treatment, and prognosis. Future clinical trials utilizing FOSCC as a tumor model may facilitate translation of preclinical cancer research for human cancer patients. © 2013 Jackie M. Wypij.


Wang Y.,University of Illinois at Urbana - Champaign | Mori G.,Simon Fraser University
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2011

We present a discriminative part-based approach for human action recognition from video sequences using motion features. Our model is based on the recently proposed hidden conditional random field (HCRF) for object recognition. Similarly to HCRF for object recognition, we model a human action by a flexible constellation of parts conditioned on image observations. Differently from object recognition, our model combines both large-scale global features and local patch features to distinguish various actions. Our experimental results show that our model is comparable to other state-of-the-art approaches in action recognition. In particular, our experimental results demonstrate that combining large-scale global features and local patch features performs significantly better than directly applying HCRF on local patches alone. We also propose an alternative for learning the parameters of an HCRF model in a max-margin framework. We call this method the max-margin hidden conditional random field (MMHCRF). We demonstrate that MMHCRF outperforms HCRF in human action recognition. In addition, MMHCRF can handle a much broader range of complex hidden structures arising in various problems in computer vision. © 2011 IEEE.


Liberzon D.,University of Illinois at Urbana - Champaign | Trenn S.,University of Kaiserslautern
Automatica | Year: 2012

We study switched nonlinear differential algebraic equations (DAEs) with respect to existence and nature of solutions as well as stability. We utilize piecewise-smooth distributions introduced in earlier work for linear switched DAEs to establish a solution framework for switched nonlinear DAEs. In particular, we allow induced jumps in the solutions. To study stability, we first generalize Lyapunov's direct method to non-switched DAEs and afterwards obtain Lyapunov criteria for asymptotic stability of switched DAEs. Developing appropriate generalizations of the concepts of a common Lyapunov function and multiple Lyapunov functions for DAEs, we derive sufficient conditions for asymptotic stability under arbitrary switching and under sufficiently slow average dwell-time switching, respectively. © 2012 Elsevier Ltd. All rights reserved.


Tan A.S.L.,University of Pennsylvania | Bigman C.A.,University of Illinois at Urbana - Champaign
American Journal of Preventive Medicine | Year: 2014

Background Electronic cigarettes, or e-cigarettes, are increasingly advertised as replacements for regular cigarettes or cessation aids for smokers. Purpose To describe the prevalence and correlates of e-cigarette awareness and perceived harmfulness among U.S. adults and analyze whether these variables are associated with smokers' past-year quit attempts and intention to quit. Methods Data were obtained from the Health Information National Trends Survey (HINTS 4 Cycle 2), conducted from October 2012 to January 2013. Data analyses were performed from June to August 2013. Results Overall, 77% of respondents were aware of e-cigarettes. Of these, 51% believed e-cigarettes were less harmful than cigarettes. Younger, white (compared with Hispanic), more educated respondents and current or former smokers (compared with non-smokers) were more likely to be aware of e-cigarettes. Among those who were aware of e-cigarettes, younger, more educated respondents and current smokers (compared with former and non-smokers) were more likely to believe that e-cigarettes were less harmful. Awareness and perceived harm were not associated with smokers' past year quit attempts or intention to quit. Conclusions Overall e-cigarette awareness increased whereas the proportion of smokers who perceived less harm of e-cigarettes declined compared with earlier surveys. However, awareness and perceived harm of e-cigarettes did not show evidence of promoting smoking cessation at the population level. © 2014 American Journal of Preventive Medicine.


Dey S.,Indian Institute of Technology Delhi | Di Girolamo L.,University of Illinois at Urbana - Champaign
Geophysical Research Letters | Year: 2011

Changing atmospheric aerosol properties caused by anthropogenic activities carries serious implications for climate change and human health. The launch of the Multi-angle Imaging SpectroRadiometer (MISR) onboard Terra spacecraft more than a decade ago provides the first capability to monitor several physical properties of aerosols over land from space. We use ten years (Mar 2000-Feb 2010) of observations from MISR to quantify seasonal linear trends of aerosol optical depth () segregated by particle size and shape over the Indian subcontinent. Here we show that many regions (referred to here as hotspots) have statistically significant (i.e., p < 0.05) seasonal linear trends in , with seasonal increasing in the range 0.1-0.4 in the last decade. These hotspots are associated with urban centers and densely-populated rural areas. Based on particle size and shape, we demonstrate that the trends, facilitated by topography and synoptic scale meteorology, are attributed to a significant rise in anthropogenic particles with additional contribution of natural particles in the rural and oceanic regions. The spatial and seasonal patterns of trends suggest greater complexity in quantifying potential aerosol-induced regional climate and air quality effects, particularly at coarser scales. Copyright 2011 by the American Geophysical Union.


Lavaux G.,University of Illinois at Urbana - Champaign
Monthly Notices of the Royal Astronomical Society | Year: 2010

We use the formalism of constrained Gaussian random fields to compute a precise large-scale simulation of the 60 h-1 Mpc volume of our local Universe. We derive the constraints from the reconstructed peculiar velocities of the 2MASS (Two Micron All-Sky Survey) Redshift Survey (2MRS). We obtain a correlation of 0.97 between the log density field of the dark matter distribution of the simulation and the log density of observed galaxies of the local Universe. We achieve a good comparison of the simulated velocity field to the observed velocity field obtained from the galaxy distances of the Nearby Galaxy Catalog 3000 km s-1 (NBG-3k, Tully et al.). At the end, we compare the two-point correlation function of both the 2MRS galaxies and the dark matter particles of the simulation. We conclude that this method is a very promising technique for exploring the dynamics and structure of the Universe in our neighbourhood. © 2010 The Author. Journal compilation © 2010 RAS.


Chen X.,University of Illinois at Urbana - Champaign
Optics Express | Year: 2014

Self rolled-up microtube is a natural device that may couple light vertically out of a planar photonic device. It is instructive to understand the optical resonant modes propagating inside the microtube waveguide. All previous models for the microtube resonant modes ignored the nonconcentric nature of its structure. Conformal transformation was used for the first time to address this issue and to obtain equivalent planar parallel-piped waveguide structure which in turn leads to an approximate analytical solution of the resonant modes of the tube. This work paves the way for accurately calculating the coupling coefficient between the microtube and a planar waveguide. The results calculated using this model matched very well with published experimental data and COMSOL simulation. © 2014 Optical Society of America.


Wagner L.K.,University of Illinois at Urbana - Champaign
International Journal of Quantum Chemistry | Year: 2014

Humanity faces one of its greatest challenges in the move from fossil-fuel based energy sources to alternative sources that do not produce greenhouse gases. New materials design is an important facet of the overall solution, since designed materials have the potential to increase efficiency in areas ranging from solar electricity generation to energy storage and distribution technologies. In that context, it is vital to be able to predict the properties of materials from basic physical principles. While traditional electronic structure techniques such as the ubiquitous density functional theory (DFT) are very important in this goal, there are many cases where current implementations of DFT fail in a design-important way. Among other solutions, quantum Monte Carlo techniques have emerged as a practical way to obtain predictive power for challenging materials. This perspective highlights some recent advances in this field, concentrating in particular on the effect that quantum Monte Carlo methods have and will have on our energy challenge. © 2013 Wiley Periodicals, Inc. Calculating the properties of electrons using random samples can lead to much higher accuracy solutions of the Schröedinger equation. This class of methods, called quantum Monte Carlo methods, has begun to make a significant impact on predictive calculations for energy-relevant materials. This perspective summarizes the methods and some of their impacts. Copyright © 2013 Wiley Periodicals, Inc.


Mcmillen D.P.,University of Illinois at Urbana - Champaign
Journal of Regional Science | Year: 2012

Though standard spatial econometric models may be useful for specification testing, they rely heavily on a parametric structure that is highly sensitive to model misspecification. The commonly used spatial AR model is a form of spatial smoothing with a structure that closely resembles a semiparametric model. Nonparametric and semiparametric models are generally a preferable approach for more descriptive spatial analysis. Estimated population density functions illustrate the differences between the spatial AR model and nonparametric approaches to data smoothing. A series of Monte Carlo experiments demonstrates that nonparametric predicted values and marginal effect estimates are much more accurate then spatial AR models when the contiguity matrix is misspecified. © 2012, Wiley Periodicals, Inc.


Lee J.,University of Illinois at Urbana - Champaign
Nature Materials | Year: 2016

Within the heterogeneous architecture of tumour tissue there exists an elusive population of stem-like cells that are implicated in both recurrence and metastasis. Here, by using engineered extracellular matrices, we show that geometric features at the perimeter of tumour tissue will prime a population of cells with a stem-cell-like phenotype. These cells show characteristics of cancer stem cells in vitro, as well as enhanced tumorigenicity in murine models of primary tumour growth and pulmonary metastases. We also show that interfacial geometry modulates cell shape, adhesion through integrin α5β1, MAPK and STAT activity, and initiation of pluripotency signalling. Our results for several human cancer cell lines suggest that interfacial geometry triggers a general mechanism for the regulation of cancer-cell state. Similar to how a growing tumour can co-opt normal soluble signalling pathways, our findings demonstrate how cancer can also exploit geometry to orchestrate oncogenesis. © 2016 Nature Publishing Group


Shemonski N.D.,University of Illinois at Urbana - Champaign
Nature Photonics | Year: 2015

High-resolution in vivo imaging is of great importance for the fields of biology and medicine. The introduction of hardware-based adaptive optics (HAO) has pushed the limits of optical imaging, enabling high-resolution near diffraction-limited imaging of previously unresolvable structures. In ophthalmology, when combined with optical coherence tomography, HAO has enabled a detailed three-dimensional visualization of photoreceptor distributions and individual nerve fibre bundles in the living human retina. However, the introduction of HAO hardware and supporting software adds considerable complexity and cost to an imaging system, limiting the number of researchers and medical professionals who could benefit from the technology. Here we demonstrate a fully automated computational approach that enables high-resolution in vivo ophthalmic imaging without the need for HAO. The results demonstrate that computational methods in coherent microscopy are applicable in highly dynamic living systems. © 2015 Nature Publishing Group


Nedic A.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2011

We consider a distributed multi-agent network system where each agent has its own convex objective function, which can be evaluated with stochastic errors. The problem consists of minimizing the sum of the agent functions over a commonly known constraint set, but without a central coordinator and without agents sharing the explicit form of their objectives. We propose an asynchronous broadcast-based algorithm where the communications over the network are subject to random link failures. We investigate the convergence properties of the algorithm for a diminishing (random) stepsize and a constant stepsize, where each agent chooses its own stepsize independently of the other agents. Under some standard conditions on the gradient errors, we establish almost sure convergence of the method to an optimal point for diminishing stepsize. For constant stepsize, we establish some error bounds on the expected distance from the optimal point and the expected function value. We also provide numerical results. © 2006 IEEE.


Muller M.A.,University of Stuttgart | Liberzon D.,University of Illinois at Urbana - Champaign
Automatica | Year: 2012

In this paper, the concepts of input/output-to-state stability (IOSS) and state-norm estimators are considered for switched nonlinear systems under average dwell-time switching signals. We show that when the average dwell-time is large enough, a switched system is IOSS if all of its constituent subsystems are IOSS. Moreover, under the same conditions, a non-switched state-norm estimator exists for the switched system. Furthermore, if some of the constituent subsystems are not IOSS, we show that still IOSS can be established for the switched system, if the activation time of the non-IOSS subsystems is not too big. Again, under the same conditions, a state-norm estimator exists for the switched system. However, in this case, the state-norm estimator is a switched system itself, consisting of two subsystems. We show that this state-norm estimator can be constructed such that its switching times are independent of the switching times of the switched system it is designed for. © 2012 Elsevier Ltd. All rights reserved.


Sun J.,University of Illinois at Urbana - Champaign
Nature communications | Year: 2013

Protein functions are largely affected by their conformations. This is exemplified in proteins containing modular domains. However, the evolutionary dynamics that define and adapt the conformation of such modular proteins remain elusive. Here we show that cis-interactions between the C-terminal phosphotyrosines and SH2 domain within the protein tyrosine phosphatase Shp2 can be tuned by an adaptor protein, Grb2. The competitiveness of two phosphotyrosines, namely pY542 and pY580, for cis-interaction with the same SH2 domain is governed by an antagonistic combination of contextual amino acid sequence and position of the phosphotyrosines. Specifically, pY580 with the combination of a favourable position and an adverse sequence has an overall advantage over pY542. Swapping the sequences of pY542 and pY580 results in one dominant form of cis-interaction and subsequently inhibits the trans-regulation by Grb2. Thus, the antagonistic combination of sequence and position may serve as a basic design principle for proteins with tunable conformations.


Ryu S.,University of Illinois at Urbana - Champaign | Zhang S.-C.,Stanford University
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We discuss (2+1)-dimensional topological superconductors with N f left- and right-moving Majorana edge modes and a Z 2×Z 2 symmetry. In the absence of interactions, these phases are distinguished by an integral topological invariant N f. With interactions, the edge state in the case of N f=8 is unstable against interactions, and a Z 2×Z 2 invariant mass gap can be generated dynamically. We show that this phenomenon is closely related to the modular invariance of type II superstring theory. More generally, we show that the global gravitational anomaly of the nonchiral Majorana edge states is the physical manifestation of the bulk topological superconductors classified by Z 8. © 2012 American Physical Society.


Ming R.,University of Illinois at Urbana - Champaign | Bendahmane A.,French National Institute for Agricultural Research | Bendahmane A.,King Saud University | Renner S.S.,Ludwig Maximilians University of Munich
Annual Review of Plant Biology | Year: 2011

Sex chromosomes in land plants can evolve as a consequence of close linkage between the two sex determination genes with complementary dominance required to establish stable dioecious populations, and they are found in at least 48 species across 20 families. The sex chromosomes in hepatics, mosses, and gymnosperms are morphologically heteromorphic. In angiosperms, heteromorphic sex chromosomes are found in at least 19 species from 4 families, while homomorphic sex chromosomes occur in 20 species from 13 families. The prevalence of the XY system found in 44 out of 48 species may reflect the predominance of the evolutionary pathway from gynodioecy towards dioecy. All dioecious species have the potential to evolve sex chromosomes, and reversions back from dioecy to various forms of monoecy, gynodioecy, or androdioecy have also occurred. Such reversals may occur especially during the early stages of sex chromosome evolution before the lethality of the YY (or WW) genotype is established. Copyright © 2011 by Annual Reviews. All rights reserved.


Hilton H.H.,University of Illinois at Urbana - Champaign
Journal of Elasticity | Year: 2011

Detailed new analytical investigations are presented describing the behavior of Class I, II and III viscoelastic Poisson's ratios (PR). Their previously demonstrated dependence on stress-time histories, which lead to the inability to consider them as universal viscoelastic material properties and the incapacity to produce a general elastic-viscoelastic correspondence principle (EVCP) based, is expanded. A new Class VI PR is analytically derived from the viscoelastic constitutive relations in the Fourier transform (FT) space to achieve the proper FT form of the elastic/viscoelastic correspondence principle, i.e., the elastic-viscoelastic analogy. However, even though this PR Class is a pure universal material property function, it still fails to provide a convenient and useful path to a correspondence principle due to its inopportune constitutive form in real time space vis-à-vis a thermodynamic model with equivalent attributes. Consequently, no general EVCP involving PRs can be formulated. The derived Class VI PRs are equivalent to the defined Class III PRs with 1-D loadings (stresses). © Springer Science+Business Media B.V. 2011.


Objectives: Obesity and smoking are two leading health risk factors and consume substantial health care resources. This study estimates and tracks annual per-capita health care expenses associated with obesity and smoking among U.S. adults aged 18 years and older from 1998 to 2011. Study design: Retrospective data analysis. Methods: Individual-level data came from the National Health Interview Survey 1996-2010 waves and the Medical Expenditure Panel Survey 1998-2011 waves. Annual per-capita health care expenses associated with obesity and smoking were estimated in two-part models, accounting for individual characteristics and sampling design. Results: Obesity and smoking were associated with an increase in annual per-capita total health care expenses (2011 US$) by $1360 (95% confidence interval: $1134-$1587) and $1046 ($846-$1247), out-of-pocket expenses by $143 ($110-$176) and $70 ($37-$104), hospital inpatient expenses by $406 ($283-$529) and $405 ($291-$519), hospital outpatient expenses by $164 ($119-$210) and $95 ($52-$138), office-based medical provider service expenses by $219 ($157-$280) and $117 ($62-$172), emergency room service expenses by $45 ($28-$63) and $57 ($44-$71), and prescription expenses by $439 ($382-$496) and $251 ($199-$302), respectively. From 1998 to 2011, the estimated per-capita expenses associated with obesity and smoking increased by 25% and 30% for total health care, 41% and 48% for office-based medical provider services, 59% and 66% for emergency room services, and 62% and 70% for prescriptions but decreased by 16% and 15% for out-of-pocket health care expenses, 3% and 0.3% for inpatient care, and 6% and 2% for outpatient care, respectively. Health care expenses associated with obesity and smoking were considerably larger among women, Non-Hispanic whites, and older adults compared with their male, racial/ethnic minority, and younger counterparts. Conclusions: Health care costs associated with obesity and smoking are substantial and increased noticeably during 1998-2011. They also vary significantly across gender, race/ethnicity and age. © 2014 The Royal Society for Public Health.


Cheeseman J.M.,University of Illinois at Urbana - Champaign
Plant and Soil | Year: 2012

Background and aims: The establishment of Rhizophoracean mangroves usually involves a transition from a horizontal to vertical orientation. Neither how this occurs nor the possible associated ecological benefits and costs have previously been considered. Methods: The "righting" of red mangrove (Rhizophora mangle L.) propagules was studied using frequent observation and time lapse photography under growth chamber and greenhouse conditions. Rates of leaf appearance were analyzed as functions of substrate, propagule placement, propagule orientation and salinity. Results: Propagule righting progressed in four phases. First, propagules alternately elevated and relaxed in a diurnal cycle. Next, propagules developed upward curvature, centered approximately two-thirds of the way between the base and tip; curvature developed and relaxed in 24 h cycles. Third, the distal portion straightened and a second center of curvature developed at the base, elevating the whole propagule. Finally, the epicotyl swelled, the stem elongated and leaves unfolded. If bases were in contact with the substrate, initial orientation had no effect on leaf opening. However, propagules without that contact experienced delays throughout the cycle. The delays were longer, initially, at higher salinity. Conclusions: R. mangle propagules are both physiologically and phenotypically highly flexible. This improves their chances of successful establishment in a heterogeneous, unpredictable, and often, high energy environment. © 2012 Springer Science+Business Media B.V.


Goh J.O.,University of Illinois at Urbana - Champaign
Aging and Disease | Year: 2011

Aging is associated with myriad changes in behavioral performance and brain structure and function. Given this complex interplay of brain and behavior, two streams of findings are reviewed here that show that aging is generally associated with dedifferentiated neural processes, and also changes in functional connectivity. This article considers an integrated view of how such age-related dedifferentiation of neural function and changes in functional connectivity are related, highlighting some recent findings on differences in small-world architecture in the functional connectivity of young and older adults. These findings suggest that both neural connectivity and the organization of these connections are important determinants of processing efficiency with aging that may be the underlying mechanisms for dedifferentiation. Thus, the evaluation of the neurocognitive effects of aging on functional connectivity provides an alternative framework that captures the behavioral and brain changes that are observed in cognitive aging.


Huang X.,University of Illinois at Urbana - Champaign
Biointerphases | Year: 2012

We present the design and use of an ultrathin, stretchable sensor system capable of conformal lamination onto the skin, for precision measurement and spatial mapping of levels of hydration. This device, which we refer to as a class of 'epidermal electronics' due to its 'skin-like' construction and mode of intimate integration with the body, contains miniaturized arrays of impedance-measurement electrodes arranged in a differential configuration to compensate for common-mode disturbances. Experimental results obtained with different frequencies and sensor geometries demonstrate excellent precision and accuracy, as benchmarked against conventional, commercial devices. The reversible, non-invasive soft contact of this device with the skin makes its operation appealing for applications ranging from skin care, to athletic monitoring to health/wellness assessment.


Rauchfuss T.B.,University of Illinois at Urbana - Champaign
Accounts of Chemical Research | Year: 2015

Conspectus The [FeFe] hydrogenases (H2ases) catalyze the redox reaction that interconverts protons and H2. This area of biocatalysis has attracted attention because the metal-based chemistry is unusual, and the reactions have practical implications. The active site consists of a [4Fe-4S] cluster bridged to a [Fe2(μ-dithiolate)(CN)2(CO)3]z center (z = 1- and 2-). The dithiolate cofactor is [HN(CH2S)2]2-, called the azadithiolate ([adtH]2-). Although many derivatives of Fe2(SR)2(CO)6-xLx are electrocatalysts for the hydrogen evolution reaction (HER), most operate by slow nonbiomimetic pathways. Biomimetic hydrogenogenesis is thought to involve intermediates, wherein the hydride substrate is adjacent to the amine of the adtH, being bonded to only one Fe center.Formation of terminal hydride complexes is favored when the diiron carbonyl models contain azadithiolate. Although unstable in the free state, the adt cofactor is stable once it is affixed to the Fe2 center. It can be prepared by alkylation of Fe2(SH)2(CO)6 with formaldehyde in the presence of ammonia (to give adtH derivatives) or amines (to give adtR derivatives). Weak acids protonate Fe2(adtR)(CO)2(PR3)4 to give terminal hydrido (term-H) complexes. In contrast, protonation of the related 1,3-propanedithiolate (pdt2-) complexes Fe2(pdt)(CO)2(PR3)4 requires strong acids. The amine in the azadithiolate is a kinetically fast base, relaying protons to and from the iron, which is a kinetically slow base. The crystal structure of the doubly protonated model [(term-H)Fe2(HadtH)(CO)2(dppv)2]2+ confirms the presence of both ammonium and terminal hydrido centers, which interact through a dihydrogen bond (dppv = cis-C2H2(PPh2)2). DFT calculations indicate that this H - -H interaction is sensitive to the counterions and is strengthened upon reduction of the diiron center. For the monoprotonated models, the hydride [(term-H)Fe2(adtH)(CO)2(dppv)2]+ exists in equilibrium with the ammonium tautomer [Fe2(HadtH)(CO)2(dppv)2]+. Both [(term-H)Fe2(HadtH)(CO)2(dppv)2]2+ and [(term-H)Fe2(adtH)(CO)2(dppv)2]+ are highly active electrocatalysts for HER. Catalysis is initiated by reduction of the diferrous center, which induces coupling of the protic ammonium center and the hydride ligand. In contrast, the propanedithiolate [(term-H)Fe2(pdt)(CO)2(dppv)2]+ is a poor electrocatalyst for HER.Oxidation of H2 has been demonstrated, starting with models for the oxidized state ("Hox"), for example, [Fe2(adtH)(CO)3(dppv)(PMe3)]+. Featuring a distorted Fe(II)Fe(I) center, this Hox model reacts slowly with high pressures of H2 to give [(μ-H)Fe2(adtH)(CO)3(dppv)(PMe3)]+. Highlighting the role of the proton relay, the propanedithiolate [Fe2(pdt)(CO)3(dppv)(PMe3)]+ is unreactive toward H2. The Hox-model + H2 reaction is accelerated in the presence of ferrocenium salts, which simulate the role of the attached [4Fe-4S] cluster. The redox-complemented complex [Fe2(adtBn)(CO)3(dppv)(FcP∗)]n+ catalyzes both proton reduction and hydrogen oxidation (FcP∗ = (C5Me5)Fe(C5Me4CH2PEt2)). © 2015 American Chemical Society.


Anastasio T.J.,University of Illinois at Urbana - Champaign
Journal of Theoretical Biology | Year: 2011

Alzheimer Disease (AD) is the most prevalent form of dementia and the sixth leading cause of death in developed world. A substantial amount of data concerning the pathogenesis of this neurological disorder is available, but the complexity of the interactions they reveal makes it difficult to reason about them. This paper describes a computational model that represents known facts concerning AD pathophysiology and demonstrates the implications of those facts in the aggregate. The computational model is written in a mathematical language known as Maude. Because a Maude specification is an executable mathematical theory, it can be used not only to simulate but also to logically analyze the system it models. This model is based on the amyloid hypothesis, which posits that AD results from the build-up of the peptide beta-amyloid. The AD model represents beta-amyloid regulation, and shows through model analysis how that regulation can be disrupted through the interaction of pathological processes such as cerebrovascular insufficiency, inflammation, and oxidative stress. The model demonstrates many other effects that depend in complex ways on interactions between elements. It also shows how treatments directed at multiple targets could be more effective at reducing beta-amyloid than single-target therapies, and it makes several experimentally testable predictions. The work demonstrates that modeling AD as an executable mathematical theory using a specification language such as Maude is a viable adjunct to experiment, which allows insights and predictions to be derived that take more of the relevant biology into account than would be possible without the aid of the computational model. © 2011 Elsevier Ltd.


Helton J.J.,University of Illinois at Urbana - Champaign
Child Abuse and Neglect | Year: 2011

Objective: This study examined the relative risk of placement disruption for 3-10 year-old children placed in out-of-home care based on the biological relatedness of the placement caregiver and child disability status: no disability, a non-behavioral disability only, a behavioral disability only, or both a non-behavioral and behavioral disability. Methods: Data were used from the baseline and 36 month follow-up of the National Survey of Child and Adolescent Well-Being, a national probability study of children investigated for child abuse and neglect in the United States. Disability status was derived using several different nationally-normed measures of language development, daily-living skills, social skills, and behavioral problems. Results: Around 1 in 4 children placed in out-of-home care experienced a disruption. Placement with kin decreased the likelihood of disruption for a majority of children, and children with different types of disabilities were no more or less likely to disrupt in kinship care compared to children with no disability. Older children with a behavioral disability only or both a non-behavioral and behavioral disability were more likely to disrupt compared to younger regardless of placement. Conclusion: The study findings suggest that maltreated children placed with kin will be afforded the same stability provided to children without a disability. © 2011 Elsevier Ltd.


Silverman S.K.,University of Illinois at Urbana - Champaign
Accounts of Chemical Research | Year: 2015

ConspectusCatalysis is a fundamental chemical concept, and many kinds of catalysts have considerable practical value. Developing entirely new catalysts is an exciting challenge. Rational design and screening have provided many new small-molecule catalysts, and directed evolution has been used to optimize or redefine the function of many protein enzymes. However, these approaches have inherent limitations that prompt the pursuit of different kinds of catalysts using other experimental methods.Nature evolved RNA enzymes, or ribozymes, for key catalytic roles that in modern biology are limited to phosphodiester cleavage/ligation and amide bond formation. Artificial DNA enzymes, or deoxyribozymes, have great promise for a broad range of catalytic activities. They can be identified from unbiased (random) sequence populations as long as the appropriate in vitro selection strategies can be implemented for their identification. Notably, in vitro selection is different in key conceptual and practical ways from rational design, screening, and directed evolution. This Account describes the development by in vitro selection of DNA catalysts for many different kinds of covalent modification reactions of peptide and protein substrates, inspired in part by our earlier work with DNA-catalyzed RNA ligation reactions.In one set of studies, we have sought DNA-catalyzed peptide backbone cleavage, with the long-term goal of artificial DNA-based proteases. We originally anticipated that amide hydrolysis should be readily achieved, but in vitro selection instead surprisingly led to deoxyribozymes for DNA phosphodiester hydrolysis; this was unexpected because uncatalyzed amide bond hydrolysis is 105-fold faster. After developing a suitable selection approach that actively avoids DNA hydrolysis, we were able to identify deoxyribozymes for hydrolysis of esters and aromatic amides (anilides). Aliphatic amide cleavage remains an ongoing focus, including via inclusion of chemically modified DNA nucleotides in the catalyst, which we have recently found to enable this cleavage reaction. In numerous other efforts, we have investigated DNA-catalyzed peptide side chain modification reactions. Key successes include nucleopeptide formation (attachment of oligonucleotides to peptide side chains) and phosphatase and kinase activities (removal and attachment of phosphoryl groups to side chains).Through all of these efforts, we have learned the importance of careful selection design, including the frequent need to develop specific "capture" reactions that enable the selection process to provide only those DNA sequences that have the desired catalytic functions. We have established strategies for identifying deoxyribozymes that accept discrete peptide and protein substrates, and we have obtained data to inform the key choice of random region length at the outset of selection experiments. Finally, we have demonstrated the viability of modular deoxyribozymes that include a small-molecule-binding aptamer domain, although the value of such modularity is found to be minimal, with implications for many selection endeavors.Advances such as those summarized in this Account reveal that DNA has considerable catalytic abilities for biochemically relevant reactions, specifically including covalent protein modifications. Moreover, DNA has substantially different, and in many ways better, characteristics than do small molecules or proteins for a catalyst that is obtained "from scratch" without demanding any existing information on catalyst structure or mechanism. Therefore, prospects are very strong for continued development and eventual practical applications of deoxyribozymes for peptide and protein modification. © 2015 American Chemical Society.


Woon D.E.,University of Illinois at Urbana - Champaign
Astrophysical Journal | Year: 2011

A new family of very favorable reaction pathways is explored involving the deposition of ions on icy grain mantles with very low energies. Quantum chemical cluster calculations at the MP2/6-31+G** level in 4H2O clusters and at the B3LYP/6-31+G** level in 17H2O clusters indicate that HCO+ and CH 3+ are able to react spontaneously with one of the water molecules in the cluster to form protonated formic acid (HCOOH2 +) and protonated methanol (CH3OH2 +), respectively. It is furthermore found that these initial adducts spontaneously transfer their excess protons to the cluster to form neutral formic acid and methanol, plus solvated hydronium, H3O+. In the final case, if a CO molecule is bound to the surface of the cluster, OH+ may react with it to form protonated carbon dioxide (HCO 2+), which then loses its proton to yield CO2 and H3O+. In the present model, all of these processes were found to occur with no barriers. Discussion includes the analogous gas-phase processes, which have been considered in previous studies, as well as the competitive abstraction pathway for HCO+ + H2O. © 2011. The American Astronomical Society. All rights reserved. Printedin the U.S.A.


Motl R.W.,University of Illinois at Urbana - Champaign
Multiple Sclerosis Journal | Year: 2014

Supervised exercise training has substantial benefits for persons with multiple sclerosis (MS), yet 80% of those with MS do not meet recommended levels of moderate-to-vigorous physical activity (MVPA). This same problem persisted for decades in the general population of adults and prompted a paradigm shift away from "exercise training for fitness" toward "physical activity for health." The paradigm shift reflects a public health approach of promoting lifestyle physical activity through behavioral interventions that teach people the skills, techniques, and strategies based on established theories for modifying and self-regulating health behaviors. This paper describes: (a) the definitions of and difference between structured exercise training and lifestyle physical activity; (b) the importance and potential impact of the paradigm shift; (c) consequences of lifestyle physical activity in MS; and (d) behavioral interventions for changing lifestyle physical activity in MS. The paper introduces the "new kid on the MS block" with the hope that lifestyle physical activity might become an accepted partner alongside exercise training for inclusion in comprehensive MS care. © The Author(s) 2014.


Motl R.W.,University of Illinois at Urbana - Champaign
Exercise and Sport Sciences Reviews | Year: 2010

Multiple sclerosis (MS) is a neurological disease that may result in the progressive worsening of disability. Recent research has identified physical activity as a behavioral correlate of disability in MS. The current review highlights that previous research has generally included samples with minimal disability and provides a rationale for considering physical activity as an influence of disability in the second stage of MS. Copyright © 2010 by the American College of Sports Medicine.


Meseguer J.,University of Illinois at Urbana - Champaign
Journal of Logic and Algebraic Programming | Year: 2012

Rewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems. © 2011 Elsevier Inc. All rights reserved.


Sreenivas R.S.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2012

We first show that the existence, or nonexistence, of a supervisory policy that enforces liveness in an arbitrary Petri net (PN) is not semidecidable. Following this, we show that this is not the case if we restrict our attention to an arbitrary, partially controlled, free-choice Petri net (FCPN). Starting from the observation that the set of initial markings for which there is a supervisory policy that enforces liveness in a free-choice structure is right-closed, we present a string of observations that eventually lead to the conclusion that the existence of a supervisory policy that enforces liveness in an arbitrary FCPN is decidable. The paper concludes with some suggested directions for future research. © 2011 IEEE.


Wang S.,University of Illinois at Urbana - Champaign
Annals of the Association of American Geographers | Year: 2010

Cyberinfrastructure (CI) integrates distributed information and communication technologies for coordinated knowledge discovery. The purpose of this article is to develop a CyberGIS framework for the synthesis of CI, geographic information systems (GIS), and spatial analysis (broadly including spatial modeling). This framework focuses on enabling computationally intensive and collaborative geographic problem solving. The article describes new trends in the development and use of CyberGIS while illustrating particular CyberGIS components. Spatial middleware glues CyberGIS components and corresponding services while managing the complexity of generic CI middleware. Spatial middleware, tailored to GIS and spatial analysis, is developed to capture important spatial characteristics of problems through the spatially explicit representation of computing, data, and communication intensity (collectively termed computational intensity), which enables GIS and spatial analysis to locate, allocate, and use CI resources effectively and efficiently. A CyberGIS implementation-GISolve-is developed to systematically integrate CI capabilities, including high-performance and distributed computing, data management and visualization, and virtual organization support. Currently, GISolve is deployed on the National Science Foundation TeraGrid, a key element of the U.S. and worldwide CI. A case study, motivated by an application in which geographic patterns of the impact of global climate change on large-scale crop yields are examined in the United States, focuses on assessing the computational performance of GISolve on resolving the computational intensity of a widely used spatial interpolation analysis that is conducted in a collaborative fashion. Computational experiments demonstrate that GISolve achieves a high-performance, distributed, and collaborative CyberGIS implementation. © 2010 by Association of American Geographers.


Allen M.R.,University of Illinois at Urbana - Champaign
Limnology and Oceanography | Year: 2010

To test the hypothesis that variation in hatching and survival of Daphnia dormant eggs is fostered by genetic differences among populations, rather than system-specific availability of environmental cues, I measured hatching and egg survival rates for Daphnia from 22 shallow, Ashless ponds in the midwestern U.S.A. Although all eggs were incubated at a water depth of 0.75 m or less in their natal pond, hatching rates varied between 5% and 90% and survival rates of eggs remaining in the egg bank ranged from 7% to 72%. There was no significant relationship between hatching and environmental cues such as light, oxygen content, or conductivity, although a negative relationship with depth was observed. Reciprocal transplant experiments quantified genetic and environmental influences on dormancy and survival, revealing strong population-by-host environment interactions. Thus, plasticity to environmental cues and genetic or maternal effects likely interact to determine hatching and survival rates in the field. © 2010, by the American Society of Limnology and Oceanography, Inc.


Schreckinger M.E.,University of Illinois at Urbana - Champaign
Journal of medicinal food | Year: 2010

Dietary intake of berry fruits has been demonstrated to positively impact human health. Interest in exploring new and exotic types of berries has grown in recent years. This article provides botanical descriptions and reviews the chemistry, biological activities, and commercialization of berry-producing plants from South America, specifically Aristotelia chilensis, Euterpe oleracea, Malpighia emarginata, Ugni molinae, Fragaria chiloensis, Rubus glaucus, Rubus adenotrichus, and Vaccinium floribundum. These species possess a rich and diversified composition of bioactive compounds with health-promoting properties. The most significant health benefits have been attributed to phenolic compounds and vitamin C, potentially protective against cardiovascular disease and cancer. Although both traditional folk medicine and composition of these berries suggest significant health benefits, few studies to date have investigated these potentials.


Liechty J.M.,University of Illinois at Urbana - Champaign
Journal of Adolescent Health | Year: 2010

Purpose: To examine the relationship between body image distortion (BID) and onset of three types of weight loss behavior among nonoverweight girls in the United States. Methods: Data were from the National Longitudinal Study of Adolescent Health (Add Health) (n = 20,745) and included 5,173 nonoverweight (body mass index [BMI] < 85th percentile) adolescent females aged 11-19 years who completed Wave I and II interviews. Actual and perceived weight statuses were compared to assess BID. Logistic regression was used to predict onset of three types of weight loss behaviors at Wave II from BID at Wave I, adjusting for Wave I weight loss behaviors and demographics. Results: At Wave I, 85% of nonoverweight girls engaged in weight control behaviors, and 29% displayed BID (i.e., overestimation of weight status). When compared to girls without BID, those with BID at Wave I had 4.3 times greater odds of onset of extreme weight loss behavior (e.g., vomiting, laxatives, diet pills) (OR = 4.5, CI = 2.44-7.42) and 2.3 times higher odds of onset of dieting to control weight (OR = 2.30, CI = 1.72-3.06) 1 year later. Girls who practiced extreme weight loss had 10.7 times greater odds of continuing unsafe practices 1 year later than girls who did not (OR = 10.67, CI = 4.27-26.63). BID was unrelated to exercise for weight control. Conclusions: BID predicts onset of unsafe, but not safe, weight loss behavior among nonoverweight girls. Brief assessment of BID may help identify nonoverweight girls at risk for unsafe weight loss practices and strengthen prevention efforts. © 2010 Society for Adolescent Health and Medicine. All rights reserved.


Huang R.H.,University of Illinois at Urbana - Champaign
Biochemistry | Year: 2012

In an RNA transcript, the 2′-OH group at the 3′-terminal nucleotide is unique as it is the only 2′-OH group that is adjacent to a 3′-OH group instead of a phosphate backbone. The 2′-OH group at the 3′-terminal nucleotide of certain RNAs is methylated in vivo, which is acheived by a methyltransferase named Hen1 that is mechanistically distinct from other known RNA 2′-O-methyltransferases. In eukaryotic organisms, 3′-terminal 2′-O-methylation of small RNAs stabilizes these small RNAs for RNA interference (RNAi). In bacteria, the same methylation during RNA repair results in repaired RNA resisting future damage at the site of repair. Although the chemistry performed by the eukaryotic and bacterial Hen1 is the same, the mechanisms of how RNA is stabilized as a result of the 3′-terminal 2′-O-methylation are different between the eukaryotic RNAi and the bacterial RNA repair. In this review, I will discuss the distribution of Hen1 in living organisms, the classification of Hen1 into four subfamilies, the structure and mechanism of Hen1 that allows it to conduct RNA 3′-terminal 2′-O-methylation, and the possible evolutionary origin of Hen1 present in bacterial and eukaryotic organisms. © 2012 American Chemical Society.


Liu G.L.,University of Illinois at Urbana - Champaign
IEEE Journal on Selected Topics in Quantum Electronics | Year: 2010

Metallic nanoparticles have a strong localized plasmon resonance that is influenced by the physical properties of the nanoparticles and their immediate ambient environment. Electromagnetic field and plasmon energy can also be manipulated by engineering nanoparticle plasmonic structures to concentrate and transport the electromagnetic energy, as well as by transferring the plasmon energy. If coupled with chemical and biological molecules on the surfaces, nanoplasmonic particles and related structures can be used to detect and measure static and dynamic molecular interactions in intro and in vivo. The nanoplasmonic particle molecular sensor is an emerging research tool to help in answering questions of sophisticated genetic processing and cellular signaling mechanisms, as well as early diagnostic imaging of human diseases. The optical molecular sensing enhanced by plasmonic nanoparticles is discussed in the aspects of fundamental theories, nanofabrication, optical spectroscopy, and imaging. Many biomedical applications are also reviewed. © 2006 IEEE.


Chemla Y.R.,University of Illinois at Urbana - Champaign
Physical Chemistry Chemical Physics | Year: 2010

Nearly all aspects of nucleic acid metabolism involve motor proteins. This diverse group of enzymes, which includes DNA and RNA polymerases, the ribosome, helicases, and other translocases, converts chemical energy in the form of bond hydrolysis into concerted motion along nucleic acid filaments. The direct observation of this motion at its fundamental distance scale of one base pair has required the development of new ultrasensitive techniques. Recent advances in optical traps have now made these length scales, once the exclusive realm of crystallographic techniques, accessible. Several new studies using optical traps have revealed for the first time how motor proteins translocate along their substrates in a stepwise fashion. Though these techniques have only begun to be applied to biological problems, the unprecedented access into nucleic acid motor protein movement has already provided important insights into their mechanism. In this perspective, we review these advances and offer our view on the future of this exciting development. © 2010 the Owner Societies.


Slichter C.P.,University of Illinois at Urbana - Champaign
Physical Chemistry Chemical Physics | Year: 2010

The paper gives some background about prewar studies of paramagnetic relaxation, the author's postwar measurements of paramagnetic relaxation using 3 cm microwaves, the beginning studies of alkali metal NMR at Illinois, Overhauser's arrival and proposal, the discovery of the ESR of conduction electrons, the experiment confirming his idea in Li and Na metals, then in solutions of Na atoms in liquid ammonia, and the realization that a form of Overhauser effect might be seen when several isotopes were present in cases where atoms were mobile. Two other experiments at Illinois inspired by the Overhauser experiments are briefly described: measurement of the spin susceptibility of conduction electrons and measurement of spin-lattice relaxation times in superconductors. © 2010 the Owner Societies.


Orlean P.,University of Illinois at Urbana - Champaign
Genetics | Year: 2012

The wall gives a Saccharomyces cerevisiae cell its osmotic integrity; defines cell shape during budding growth, mating, sporulation, and pseudohypha formation; and presents adhesive glycoproteins to other yeast cells. The wall consists of β1,3- and β 1,6-glucans, a small amount of chitin, and many different proteins that may bear N- and O-linked glycans and a glycolipid anchor. These components become cross-linked in various ways to form higher-order complexes. Wall composition and degree of cross-linking vary during growth and development and change in response to cell wall stress. This article reviews wall biogenesis in vegetative cells, covering the structure of wall components and how they are cross-linked; the biosynthesis of N- and O-linked glycans, glycosylphosphatidylinositol membrane anchors, β1,3- and β1,6-linked glucans, and chitin; the reactions that cross-link wall components; and the possible functions of enzymatic and nonenzymatic cell wall proteins. © 2012 the Genetics Society of America.


Rogers J.A.,University of Illinois at Urbana - Champaign
MRS Bulletin | Year: 2014

New methods for the synthesis and deterministic assembly of advanced classes of nanomaterials enable integration of high-performence semiconductors with elastomeric substrates. These capabilities provide the foundations for a high-performance electronic and optoelectronic technology that can offer linear elastic mechanical responses to large strain deformations. The results create new opportunities in materials and device engineering, with important consequences in fields ranging from biomedicine to machine vision. This article summarizes the key materials science concepts and presents illustrative examples of their recent use in injectable, cellular-scale optoelectronic devices and in hemispherical compound eye cameras. © Materials Research Society 2014.


Wang W.,Massachusetts Institute of Technology | Oldfield E.,University of Illinois at Urbana - Champaign
Angewandte Chemie - International Edition | Year: 2014

Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4S4] proteins that are not produced by humans and catalyze 2 H+/ 2 e- reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4S4] clusters in proteins. A mission based on inside information: The methylerythritol phosphate pathway is an attractive anti-infective drug target. The last two enzymes of this pathway, IspG and IspH, are [Fe4S4] proteins that catalyze 2 H+/2 e- dehydroxylation reactions. Recent progress in the elucidation of their biosynthetic mechanisms opens up new routes to the design of inhibitors that target these [Fe 4S4] enzymes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Nienhaus K.,Karlsruhe Institute of Technology | Ulrich Nienhaus G.,Karlsruhe Institute of Technology | Ulrich Nienhaus G.,University of Illinois at Urbana - Champaign
Chemical Society Reviews | Year: 2014

Fluorescent proteins (FPs) from the GFP family have become indispensable as marker tools for imaging live cells, tissues and entire organisms. A wide variety of these proteins have been isolated from natural sources and engineered to optimize their properties as genetically encoded markers. Here we review recent developments in this field. A special focus is placed on photoactivatable FPs, for which the fluorescence emission can be controlled by light irradiation at specific wavelengths. They enable regional optical marking in pulse-chase experiments on live cells and tissues, and they are essential marker tools for live-cell optical imaging with super-resolution. Photoconvertible FPs, which can be activated irreversibly via a photo-induced chemical reaction that either turns on their emission or changes their emission wavelength, are excellent markers for localization-based super-resolution microscopy (e.g., PALM). Patterned illumination microscopy (e.g., RESOLFT), however, requires markers that can be reversibly photoactivated many times. Photoswitchable FPs can be toggled repeatedly between a fluorescent and a non-fluorescent state by means of a light-induced chromophore isomerization coupled to a protonation reaction. We discuss the mechanistic origins of the effect and illustrate how photoswitchable FPs are employed in RESOLFT imaging. For this purpose, special FP variants with low switching fatigue have been introduced in recent years. Despite nearly two decades of FP engineering by many laboratories, there is still room for further improvement of these important markers for live cell imaging. © 2014 The Royal Society of Chemistry.


Braun P.V.,University of Illinois at Urbana - Champaign
Chemistry of Materials | Year: 2014

This Perspective overviews many of the developments in templated porous three-dimensional photonics, with a particular focus on functional architectures, and provides suggestions for future opportunities for research. A significant diversity of 3D structures is available today with characteristic dimensions appropriate for providing strong light-matter interactions, in no small part due to recent advances in 3D patterning techniques. However, the optical functionality of these structures has generally remained limited. Advances in materials chemistry have the opportunity to dramatically increase the function of templated 3D photonics, and a few examples of highly functional templated 3D photonics for sensing, solar energy harvesting, optical metamaterials, and light emission are presented as first examples of success. © 2013 American Chemical Society.


Kuhlman T.E.,Princeton University | Kuhlman T.E.,University of Illinois at Urbana - Champaign | Cox E.C.,Princeton University
Molecular Systems Biology | Year: 2012

The diffusion coefficient of the transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D=0.4μm2/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. Here, we test this expectation of spatial homogeneity by single-molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion that can reconcile these results with previous measurements of LacI diffusion, and we discuss the implications of these findings for gene regulation in bacteria and eukaryotes. © 2012 EMBO and Macmillan Publishers Limited. All rights reserved.


Rao C.V.,University of Illinois at Urbana - Champaign
Current Opinion in Biotechnology | Year: 2012

Despite substantial progress in synthetic biology, we still lack the ability to engineer anything as complex as Nature has. One of the many reasons is that we lack the requisite tools for independently controlling the expression of multiple genes in parallel. While our toolbox is still spare, the situation is rapidly changing. This opinion discusses some recent approaches and open challenges in designing orthogonal regulators of gene expression in bacteria. © 2012.


Suslick K.S.,University of Illinois at Urbana - Champaign
Current Opinion in Chemical Biology | Year: 2012

Much of our science and technology relies on the visualization of complex data, and chemical biology, more than most fields, often deals with complex datasets. There are, however, other ways of making information available to our senses beyond the visual. Rare individuals naturally have sensory crossover, whose synesthesia permits them, for example, to see colors or shapes when hearing sounds or to sense a specific taste with a specific word. Many scientists, technologists and inventors, however, make a conscious attempt to convert one type of sensory-like input to a different sensory output. A laser light show, for example, converts sound to sight; infrared imaging converts heat to sight. Two recent examples of such intentional synesthesia are discussed in this context: sight-tasting and smell-seeing. © 2012 Elsevier Ltd.


Chaddock-Heyman L.,University of Illinois at Urbana - Champaign
Monographs of the Society for Research in Child Development | Year: 2014

In this chapter, we review literature that examines the association among physical activity, aerobic fitness, cognition, and the brain in elementary school children (ages 7-10 years). Specifically, physical activity and higher levels of aerobic fitness in children have been found to benefit brain structure, brain function, cognition, and school achievement. For example, higher fit children have larger brain volumes in the basal ganglia and hippocampus, which relate to superior performance on tasks of cognitive control and memory, respectively, when compared to their lower fit peers. Higher fit children also show superior brain function during tasks of cognitive control, better scores on tests of academic achievement, and higher performance on a real-world street crossing task, compared to lower fit and less active children. The cross-sectional findings are strengthened by a few randomized, controlled trials, which demonstrate that children randomly assigned to a physical activity intervention group show greater brain and cognitive benefits compared to a control group. Because these findings suggest that the developing brain is plastic and sensitive to lifestyle factors, we also discuss typical structural and functional brain maturation in children to provide context in which to interpret the effects of physical activity and aerobic fitness on the developing brain. This research is important because children are becoming increasingly sedentary, physically inactive, and unfit. An important goal of this review is to emphasize the importance of physical activity and aerobic fitness for the cognitive and brain health of today's youth. © 2014 The Society for Research in Child Development, Inc.


Shang L.,Karlsruhe Institute of Technology | Dong S.,CAS Changchun Institute of Applied Chemistry | Nienhaus G.U.,Karlsruhe Institute of Technology | Nienhaus G.U.,University of Illinois at Urbana - Champaign
Nano Today | Year: 2011

Recent advances in nanotechnology have given rise to a new class of fluorescent labels, fluorescent metal nanoclusters, e.g., Au and Ag. These nanoclusters are of significant interest because they provide the missing link between atomic and nanoparticle behavior in metals. Composed of a few to a hundred atoms, their sizes are comparable to the Fermi wavelength of electrons, resulting in molecule-like properties including discrete electronic states and size-dependent fluorescence. Fluorescent metal nanoclusters have an attractive set of features, such as ultrasmall size, good biocompatibility and excellent photostability, making them ideal fluorescent labels for biological applications. In this review, we summarize synthesis strategies of water-soluble fluorescent metal nanoclusters and their optical properties, highlight recent advances in their application for ultrasensitive biological detection and fluorescent biological imaging, and finally discuss current challenges for their potential biomedical applications. © 2011 Elsevier Ltd. All rights reserved.


Lu H.,University of Illinois at Urbana - Champaign | Chandran K.,Columbia University | Stensel D.,University of Washington
Water Research | Year: 2014

Globally, denitrification is commonly employed in biological nitrogen removal processes to enhance water quality. However, substantial knowledge gaps remain concerning the overall community structure, population dynamics and metabolism of different organic carbon sources. This systematic review provides a summary of current findings pertaining to the microbial ecology of denitrification in biological wastewater treatment processes. DNA fingerprinting-based analysis has revealed a high level of microbial diversity in denitrification reactors and highlighted the impacts of carbon sources in determining overall denitrifying community composition. Stable isotope probing, fluorescence in situ hybridization, microarrays and meta-omics further link community structure with function by identifying the functional populations and their gene regulatory patterns at the transcriptional and translational levels. This review stresses the need to integrate microbial ecology information into conventional denitrification design and operation at full-scale. Some emerging questions, from physiological mechanisms to practical solutions, for example, eliminating nitrous oxide emissions and supplementing more sustainable carbon sources than methanol, are also discussed. A combination of high-throughput approaches is next in line for thorough assessment of wastewater denitrifying community structure and function. Though denitrification is used as an example here, this synergy between microbial ecology and process engineering is applicable to other biological wastewater treatment processes. © 2014 Elsevier Ltd.


Deng L.,University of West Georgia | Poole M.S.,University of Illinois at Urbana - Champaign
MIS Quarterly: Management Information Systems | Year: 2010

This research concentrates on visual complexity and order as central factors in the design of webpages that enhance users' positive emotional reactions and facilitate desirable psychological states and behaviors. Drawing on existing theories and empirical findings in the environmental psychology, human-computer interaction, and marketing research literatures, a research model is developed to explain the relationships among visual complexity and order design features of a webpage, induced emotional responses in users, and users' approach behaviors toward the website as moderated by users' metamotivational states. A laboratory experiment was conducted to test the model and its associated hypotheses. The results of the study suggested that a web user's initial emotional responses (i.e., pleasantness and arousal), evoked by the visual complexity and order design features of a webpage when first encountered, will have carry-over effects on subsequent approach behavior toward the website. The results also revealed how webpage visual complexity and order influence users' emotions and behaviors differently when users are in different metamotivational states. The salience and importance of webpage visual complexity and order for users' feelings of pleasantness were largely dependent on users' metamotivational states.


Fu Y.,State University of New York at Buffalo | Guo G.,West Virginia University | Huang T.S.,University of Illinois at Urbana - Champaign
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2010

Human age, as an important personal trait, can be directly inferred by distinct patterns emerging from the facial appearance. Derived from rapid advances in computer graphics and machine vision, computer-based age synthesis and estimation via faces have become particularly prevalent topics recently because of their explosively emerging real-world applications, such as forensic art, electronic customer relationship management, security control and surveillance monitoring, biometrics, entertainment, and cosmetology. Age synthesis is defined to rerender a face image aesthetically with natural aging and rejuvenating effects on the individual face. Age estimation is defined to label a face image automatically with the exact age (year) or the age group (year range) of the individual face. Because of their particularity and complexity, both problems are attractive yet challenging to computer-based application system designers. Large efforts from both academia and industry have been devoted in the last a few decades. In this paper, we survey the complete state-of-the-art techniques in the face image-based age synthesis and estimation topics. Existing models, popular algorithms, system performances, technical difficulties, popular face aging databases, evaluation protocols, and promising future directions are also provided with systematic discussions. © 2006 IEEE.


Papenfort K.,Princeton University | Papenfort K.,Ludwig Maximilians University of Munich | Vanderpool C.K.,University of Illinois at Urbana - Champaign
FEMS Microbiology Reviews | Year: 2015

Bacterial small regulatory RNAs (sRNAs) are commonly known to repress gene expression by base pairing to target mRNAs. In many cases, sRNAs base pair with and sequester mRNA ribosome-binding sites, resulting in translational repression and accelerated transcript decay. In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets. However, the mechanisms underlying activation differ substantially from repression. Base pairing resulting in target activation can involve sRNA interactions with the 5' untranslated region (UTR), the coding sequence or the 3' UTR of the target mRNAs. Frequently, the activities of protein factors such as cellular ribonucleases and the RNA chaperone Hfq are required for activation. Bacterial sRNAs, including those that function as activators, frequently control stress response pathways or virulence-associated functions required for immediate responses to changing environments. This review aims to summarize recent advances in knowledge regarding target mRNA activation by bacterial sRNAs, highlighting the molecular mechanisms and biological relevance of regulation. © 2015 FEMS.


Saintillan D.,University of Illinois at Urbana - Champaign | Shelley M.J.,Courant Institute of Mathematical Sciences
Journal of the Royal Society Interface | Year: 2012

The emergence of coherent structures, large-scale flows and correlated dynamics in suspensions of motile particles such as swimming micro-organisms or artificial microswimmers is studied using direct particle simulations. A detailed model is proposed for a slender rod-like particle that propels itself in a viscous fluid by exerting a prescribed tangential stress on its surface, and a method is devised for the efficient calculation of hydrodynamic interactions in large-scale suspensions of such particles using slender-body theory and a smooth particle-mesh Ewald algorithm. Simulations are performed with periodic boundary conditions for various system sizes and suspension volume fractions, and demonstrate a transition to large-scale correlated motions in suspensions of rear-actuated swimmers, or Pushers, above a critical volume fraction or system size. This transition, which is not observed in suspensions of head-actuated swimmers, or Pullers, is seen most clearly in particle velocity and passive tracer statistics. These observations are consistent with predictions from our previous mean-field kinetic theory, one of which states that instabilities will arise in uniform isotropic suspensions of Pushers when the product of the linear system size with the suspension volume fraction exceeds a given threshold. We also find that the collective dynamics of Pushers result in giant number fluctuations, local alignment of swimmers and strongly mixing flows. Suspensions of Pullers, which evince no large-scale dynamics, nonetheless display interesting deviations from the random isotropic state. © 2011 The Royal Society.


Amir E.,University of Illinois at Urbana - Champaign
Algorithmica (New York) | Year: 2010

This paper presents algorithms whose input is an undirected graph, and whose output is a tree decomposition of width that approximates the optimal, the treewidth of that graph. The algorithms differ in their computation time and their approximation guarantees. The first algorithm works in polynomial-time and finds a factor-O(logOPT) approximation, where OPT is the treewidth of the graph. This is the first polynomial-time algorithm that approximates the optimal by a factor that does not depend on n, the number of nodes in the input graph. As a result, we get an algorithm for finding pathwidth within a factor of O(logOPT·logn) from the optimal. We also present algorithms that approximate the treewidth of a graph by constant factors of 3.66, 4, and 4.5, respectively and take time that is exponential in the treewidth. These are more efficient than previously known algorithms by an exponential factor, and are of practical interest. Finding triangulations of minimum treewidth for graphs is central to many problems in computer science. Real-world problems in artificial intelligence, VLSI design and databases are efficiently solvable if we have an efficient approximation algorithm for them. Many of those applications rely on weighted graphs. We extend our results to weighted graphs and weighted treewidth, showing similar approximation results for this more general notion. We report on experimental results confirming the effectiveness of our algorithms for large graphs associated with real-world problems. © 2008 Springer Science+Business Media, LLC.


Kwon H.D.,University of Illinois at Urbana - Champaign
Operations Research | Year: 2010

Even in the face of deteriorating and highly volatile demand, firms often invest in, rather than discard, aging technologies. To study this phenomenon, we model the firm's profit stream as a Brownian motion with negative drift. At each point in time, the firm can continue operations, or it can stop and exit the project. In addition, there is a one-time option to makean investment that boosts the project's profit rate. Using stochastic analysis, we show that the optimal policy always exists and that it is characterized by three thresholds. There are investment and exit thresholds before investment, and there is a threshold for exit after investment. We also effect a comparative statics analysis of the thresholds with respect to the drift and the volatility of the Brownian motion. When the profit boost upon investment is sufficiently large, we find a novel result: the investment threshold decreases in volatility. © 2010 INFORMS.


Layman D.K.,University of Illinois at Urbana - Champaign
Physiology & behavior | Year: 2014

The food industry is the point of final integration of consumer food choices with dietary guidelines. For more than 40 years, nutrition recommendations emphasized reducing dietary intake of animal fats, cholesterol, and protein and increasing intake of cereal grains. The food industry responded by creating a convenient, low cost and diverse food supply that featured fat-free cookies, cholesterol-free margarines, and spaghetti with artificial meat sauce. However, research focused on obesity, aging, and Metabolic Syndrome has demonstrated merits of increased dietary protein and reduced amounts of carbohydrates. Dietary guidelines have changed from a conceptual framework of a daily balance of food groups represented as building blocks in a pyramid designed to encourage consumers to avoid fat, to a plate design that creates a meal approach to nutrition and highlights protein and vegetables and minimizes grain carbohydrates. Coincident with the changing dietary guidelines, consumers are placing higher priority on foods for health and seeking foods with more protein, less sugars and minimal processing that are fresh, natural, and with fewer added ingredients. Individual food companies must adapt to changing nutrition knowledge, dietary guidelines, and consumer priorities. The impact on the food industry will be specific to each company based on their products, culture and capacity to adapt. Copyright © 2014 Elsevier Inc. All rights reserved.


Kuzminov A.,University of Illinois at Urbana - Champaign
Molecular Microbiology | Year: 2013

Summary: In both eukaryotes and prokaryotes, chromosomal DNA undergoes replication, condensation-decondensation and segregation, sequentially, in some fixed order. Other conditions, like sister-chromatid cohesion (SCC), may span several chromosomal events. One set of these chromosomal transactions within a single cell cycle constitutes the 'chromosome cycle'. For many years it was generally assumed that the prokaryotic chromosome cycle follows major phases of the eukaryotic one: -replication-condensation-segregation-(cell division)-decondensation-, with SCC of unspecified length. Eventually it became evident that, in contrast to the strictly consecutive chromosome cycle of eukaryotes, all stages of the prokaryotic chromosome cycle run concurrently. Thus, prokaryotes practice 'progressive' chromosome segregation separated from replication by a brief SCC, and all three transactions move along the chromosome at the same fast rate. In other words, in addition to replication forks, there are 'segregation forks' in prokaryotic chromosomes. Moreover, the bulk of prokaryotic DNA outside the replication-segregation transition stays compacted. I consider possible origins of this concurrent replication-segregation and outline the 'nucleoid administration' system that organizes the dynamic part of the prokaryotic chromosome cycle. © 2013 John Wiley & Sons Ltd.


Belabbas M.A.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2013

Formation control is concerned with the design of control laws that stabilize agents at given distances from each other, with the constraint that an agent's dynamics only depends on a subset of other agents. We show in this technical note that a broad class of control laws fails to stabilize a simple formation with four agents. The novelty of the approach used in this technical note lies in the use of bifurcation theory to show that, for almost all control laws, there exists a stable undesired equilibrium. © 1963-2012 IEEE.


Belabbas M.-A.,University of Illinois at Urbana - Champaign
Systems and Control Letters | Year: 2013

In the design of decentralized networked systems, it is important to know whether a given network topology can sustain stable dynamics. We consider a basic version of this problem here: given a vector space of sparse real matrices, does it contain a stable (Hurwitz) matrix? Said differently, is a feedback channel (corresponding to a non-zero entry) necessary for stabilization or can it be done without? We provide in this paper a set of necessary conditions and a set of sufficient conditions for the existence of stable matrices in a vector space of sparse matrices. We further prove some properties of the set of sparse matrix spaces that contain Hurwitz matrices. The conditions we exhibit are most easily stated in the language of graph theory, which we thus adopt in this paper. © 2013 Elsevier B.V. All rights reserved.


Oppenheim G.M.,University of Illinois at Urbana - Champaign
Journal of Experimental Psychology: Learning Memory and Cognition | Year: 2012

Corley, Brocklehurst, and Moat (2011) recently demonstrated a phonemic similarity effect for phonological errors in inner speech, claiming that it contradicted Oppenheim and Dell's (2008) characterization of inner speech as lacking subphonemic detail (e.g., features). However, finding an effect in both inner and overt speech is not the same as finding equal effects in inner and overt speech. In this response, I demonstrate that Corley et al.'s data are entirely consistent with the notion that inner speech lacks subphonemic detail and that each of their experiments exhibits a Similarity × Articulation interaction of about the same size that Oppenheim and Dell (2008, 2010) reported in their work. I further show that the major discrepancy between the labs' data lies primarily in the magnitude of the main effect of phonemic similarity and the overall efficiency of error elicitation, and demonstrate that greater similarity effects are associated with lower error rates. This leads to the conclusion that successful speech error research requires finding a sweet spot between too much randomness and not enough data. © 2012 American Psychological Association.


Degrande C.,University of Illinois at Urbana - Champaign
Journal of High Energy Physics | Year: 2014

Four independent dimension-eight operators give rise to anomalous neutral triple gauge boson interactions, one CP-even and three CP-odd. Only the CP-even operator interferes with the Standard Model for the production of a pair of on-shell neutral bosons. However, the effects are found to be tiny due mainly to the mismatch of the Z boson polarization between the productions from the SM and the new operator. Open Access, © 2014 The Authors.


Ha T.,University of Illinois at Urbana - Champaign
Cell | Year: 2013

Enormous mechanistic insight has been gained by studying the behavior of single molecules. The same approaches used to study proteins in isolation are now being leveraged to examine the changes in functional behavior that emerge when single molecules have company. © 2013 Elsevier Inc.


Ouyang Y.,University of Illinois at Urbana - Champaign
Transportmetrica B | Year: 2014

This paper analyses experiment results to show that advance demand information (ADI) strategies have the potential to counteract the bullwhip effect and reduce supply chain costs in practice. The experiments are conducted with a new web-based interactive computer simulation game, where human players assuming the roles of suppliers not only make replenishment order decisions but also negotiate for agreements on ADI provision, consumption, and compensation. The game is designed with enhanced information provision and communication channels through which negotiations are conducted strictly between neighbouring suppliers. As such, the supply chain is kept decentralised (i.e. no information is shared across supply chain stages). The effectiveness of ADI strategies is tested in a variety of settings; e.g. when supply chain parameters are heterogeneous, when suppliers have (or do not have) partial knowledge on the customer demand, and when suppliers are inexperienced with the ADI strategy. It is observed repeatedly that the ADI negotiation mechanism significantly improves the supply chain performance, reducing not only the total chain-wide cost but also every individual supplier's cost. This improvement is generally achieved by the downstream suppliers (e.g. retailer) making future order commitments (while carrying higher inventory), which allows upstream suppliers to gain sufficient cost reduction and provide compensation to the downstream suppliers. © 2014 Hong Kong Society for Transportation Studies Limited.


Holley J.L.,University of Illinois at Urbana - Champaign
Clinical Journal of the American Society of Nephrology | Year: 2012

Advance care planning was historically considered to be simply the completion of a proxy (health care surrogate designation) or instruction (living will) directive that resulted from a conversation between a patient and his or her physician. We now know that advance care planning is a much more comprehensive and dynamic patientcentered process used by patients and families to strengthen relationships, achieve control over medical care, prepare for death, and clarify goals of care. Some advance directives, notably designated health care proxy documents, remain appropriate expressions of advance care planning.Moreover, although physician orders, such as do-not-resuscitate orders and Physician Orders for Life-Sustaining Treatment, may not be strictly defined as advance directives, their completion, when appropriate, is an integral component of advance care planning. The changing health circumstances and illness trajectory characteristic of ESRD mandate that advance care planning discussions adapt to a patient's situation and thereforemust be readdressed at appropriate times and intervals. The options of withholding and withdrawing dialysis add ESRD-specific issues to advance care planning in this population and are events each nephrologist will at some time confront. Advance care planning is important throughout the spectrum of ESRD and is a part of nephrology practice that can be rewarding to nephrologists and beneficial to patients and their families. © 2012 by the American Society of Nephrology.


Deryugina T.,University of Illinois at Urbana - Champaign
Climatic Change | Year: 2013

Global warming has become a controversial public policy issue in spite of broad scientific consensus that it is real and that human activity is a contributing factor. It is likely that public consensus is also needed to support policies that might counteract it. It is therefore important to understand how people form and update their beliefs about climate change. Using unique survey data on beliefs about the occurrence of the effects of global warming, I estimate how local temperature fluctuations influence what individuals believe about these effects. I find that some features of the updating process are consistent with rational updating. I also test explicitly for the presence of several heuristics known to affect belief formation and find strong evidence for representativeness, some evidence for availability, and no evidence for spreading activation. I find that very short-run temperature fluctuations (1 day-2 weeks) have no effect on beliefs about the occurrence of global warming, but that longer-run fluctuations (1 month-1 year) are significant predictors of beliefs. Only respondents with a conservative political ideology are affected by temperature abnormalities. © 2012 Springer Science+Business Media Dordrecht.


Hammes-Schiffer S.,University of Illinois at Urbana - Champaign
Biochemistry | Year: 2013

This brief review analyzes the underlying physical principles of enzyme catalysis, with an emphasis on the role of equilibrium enzyme motions and conformational sampling. The concepts are developed in the context of three representative systems, namely, dihydrofolate reductase, ketosteroid isomerase, and soybean lipoxygenase. All of these reactions involve hydrogen transfer, but many of the concepts discussed are more generally applicable. The factors that are analyzed in this review include hydrogen tunneling, proton donor-acceptor motion, hydrogen bonding, pKa shifting, electrostatics, preorganization, reorganization, and conformational motions. The rate constant for the chemical step is determined primarily by the free energy barrier, which is related to the probability of sampling configurations conducive to the chemical reaction. According to this perspective, stochastic thermal motions lead to equilibrium conformational changes in the enzyme and ligands that result in configurations favorable for the breaking and forming of chemical bonds. For proton, hydride, and proton-coupled electron transfer reactions, typically the donor and acceptor become closer to facilitate the transfer. The impact of mutations on the catalytic rate constants can be explained in terms of the factors enumerated above. In particular, distal mutations can alter the conformational motions of the enzyme and therefore the probability of sampling configurations conducive to the chemical reaction. Methods such as vibrational Stark spectroscopy, in which environmentally sensitive probes are introduced site-specifically into the enzyme, provide further insight into these aspects of enzyme catalysis through a combination of experiments and theoretical calculations. © 2012 American Chemical Society.


Shapiro S.L.,University of Illinois at Urbana - Champaign
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

We consider a geometrically thin, Keplerian disk in the orbital plane of a binary black hole (BHBH) consisting of a spinning primary and low-mass secondary (mass ratio q1). To account for the principle effects of general relativity (GR), we propose a modification of the standard Newtonian evolution equation for the (orbit-averaged) time-varying disk surface density. In our modified equation the viscous torque in the disk is treated in full GR, while the tidal torque is handled in the Newtonian limit. Our GR-hybrid treatment is reasonable because the tidal torque is concentrated near the orbital radius of the secondary and is most important prior to binary-disk decoupling, when the orbital separation is large and resides in the weak-field regime. The tidal torque on the disk diminishes during late merger and vanishes altogether following merger. By contrast, the viscous torque drives the flow into the strong-field region and onto the primary during all epochs. Following binary coalescence, the viscous torque alone governs the time-dependent accretion onto the remnant, as well as the temporal behavior, strength and spectrum of the aftermath electromagnetic radiation from the disk. We solve our GR-hybrid equation for a representative BHBH-disk system, identify several observable EM signatures of the merger, and compare results obtained for the gas and EM radiation with those found with the Newtonian prescription. © 2013 American Physical Society.


Alto B.W.,University of Illinois at Urbana - Champaign
Journal of Medical Entomology | Year: 2011

The Asian rock pool mosquito Aedes japonicus (Theobald) inhabits natural and artificial container habitats, some of which are occupied by the native treehole mosquito Aedes triseriatus (Say), a vector of LaCrosse encephalitis virus. A laboratory experiment was used to evaluate the effects of nutrient limitation and interspecific interactions between these species. The goal was to address two related hypotheses. First, interspecific interactions between these species show competitive asymmetry with the invasive mosquito Ae. japonicus being favored over Ae. triseriatus. Second, competitive stress at the larval stage alters adult longevity. There was minimal evidence for competitive asymmetry between these two species. Mosquito and population performance showed clear negative density-dependent effects with similar effects of intra- and interspecific interactions. Only Ae. japonicus development time showed competitive asymmetry over Ae. triseriatus, providing weak support for the first hypothesis. For both species, competition resulted in lower adult longevity compared with low competition, providing support for the second hypothesis. These results suggest both species are similarly affected by intra- and interspecific competition and underscore the importance of the effects of larval competition that continue into adulthood and alter parameters important to transmission of vector-borne diseases. © 2011 Entomological Society of America.


Tuttle M.D.,University of Illinois at Urbana - Champaign
Nature Structural and Molecular Biology | Year: 2016

Misfolded α-synuclein amyloid fibrils are the principal components of Lewy bodies and neurites, hallmarks of Parkinson's disease (PD). We present a high-resolution structure of an α-synuclein fibril, in a form that induces robust pathology in primary neuronal culture, determined by solid-state NMR spectroscopy and validated by EM and X-ray fiber diffraction. Over 200 unique long-range distance restraints define a consensus structure with common amyloid features including parallel, in-register β-sheets and hydrophobic-core residues, and with substantial complexity arising from diverse structural features including an intermolecular salt bridge, a glutamine ladder, close backbone interactions involving small residues, and several steric zippers stabilizing a new orthogonal Greek-key topology. These characteristics contribute to the robust propagation of this fibril form, as supported by the structural similarity of early-onset-PD mutants. The structure provides a framework for understanding the interactions of α-synuclein with other proteins and small molecules, to aid in PD diagnosis and treatment. © 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.


Pilawa-Podgurski R.C.N.,University of Illinois at Urbana - Champaign | Perreault D.J.,Massachusetts Institute of Technology
IEEE Transactions on Power Electronics | Year: 2013

This paper explores the benefits of distributed power electronics in solar photovoltaic applications through the use of submodule integrated maximum power point trackers (MPPT). We propose a system architecture that provides a substantial increase in captured energy during partial shading conditions, while at the same time enabling significant overall cost reductions. This is achieved through direct integration of miniature MPPT power converters into existing junction boxes. We describe the design and implementation of a high-efficiency (>98%) synchronous buck MPPT converter, along with digital control techniques that ensure both local and global maximum power extraction. Through detailed experimental measurements under real-world conditions, we verify the increase in energy capture and quantify the benefits of the architecture. ©2012 IEEE.


Lopez-Pamies O.,University of Illinois at Urbana - Champaign
Journal of the Mechanics and Physics of Solids | Year: 2014

A microscopic field theory is developed with the aim of describing, explaining, and predicting the macroscopic response of elastic dielectric composites with two-phase particulate (periodic or random) microstructures under arbitrarily large deformations and electric fields. The central idea rests on the construction - via an iterated homogenization technique in finite electroelastostatics - of a specific but yet fairly general class of particulate microstructures which allow to compute exactly the homogenized response of the resulting composite materials. The theory is applicable to any choice of elastic dielectric behaviors (with possibly even or odd electroelastic coupling) for the underlying matrix and particles, and any choice of the one- and two-point correlation functions describing the microstructure. In spite of accounting for fine microscopic information, the required calculations amount to solving tractable first-order nonlinear (Hamilton-Jacobi-type) partial differential equations. As a first application of the theory, explicit results are worked out for the basic case of ideal elastic dielectrics filled with initially spherical particles that are distributed either isotropically or in chain-like formations and that are ideal elastic dielectrics themselves. The effects that the permittivity, stiffness, volume fraction, and spatial distribution of the particles have on the overall electrostrictive deformation (induced by the application of a uniaxial electric field) of the composite are discussed in detail. © 2013 Elsevier Ltd.


Freund L.B.,University of Illinois at Urbana - Champaign
Journal of the Mechanics and Physics of Solids | Year: 2014

The focus here is the growth of a planar crack in a brittle material under two dimensional plane strain conditions. The stress field surrounding the crack edge is presumed to be an elastic stress intensity factor field, or K-field, as is characteristic of such systems. However, as the observation point within the K-field approaches the crack edge, that field gradually gives way to a zone of material separation that is coplanar with the crack and that is characterized as a region of chemical bond breaking. The separation zone is spanned by a large number of identical atomic or molecular bonds resisting the influence of the surrounding stress field. The trailing edge of that zone coincides with the physical crack edge. By describing the collective response of these bonds in terms of the behavior of a generic bond and the statistical concept of survival probability, the process of material separation is followed to its end with no further requirement of a material failure condition. In this way, the physical process of material separation is related directly to the commonly measured fracture parameters for brittle materials. © 2013 Elsevier Ltd.


Hirata S.,University of Illinois at Urbana - Champaign
Theoretical Chemistry Accounts | Year: 2011

This article aims to dispel confusions about the definition of size consistency as well as some incompatibility that exists between different criteria for judging whether an electronic structure theory is size consistent and thus yields energies and other quantities having correct asymptotic size dependence. It introduces extensive and intensive diagram theorems, which provide unambiguous sufficient conditions for size consistency for extensive and intensive quantities, respectively, stipulated in terms of diagrammatic topology and vertex makeup. The underlying algebraic size-consistency criterion is described, which relies on the polynomial dependence of terms in the formalism on the number of wave vector sampling points in Brillouin-zone integrations. The physical meanings of two types of normalization of excitation amplitudes in electron-correlation theories, namely, the intermediate and standard normalization, are revealed. The amplitudes of the operator that describes an extensive quantity (the extensive operator) are subject to the intermediate normalization, while those of the operator that corresponds to an intensive quantity (the intensive operator) must be normalized. The article also introduces the extensive-intensive consistency theorem which specifies the relationship between the spaces of determinants reached by the extensive and intensive operators in a size-consistent method for intensive quantities. Furthermore, a more fundamental question is addressed as to what makes energies extensive and thus an application of thermodynamics to chemistry valid. It is shown that the energy of an electrically neutral, periodic, non-metallic solid is extensive. On this basis, a strictly size-consistent redefinition of the Hartree-Fock theory is proposed. © 2011 Springer-Verlag.


Dye M.W.G.,University of Illinois at Urbana - Champaign
Vision Research | Year: 2014

The major documented effect of auditory deprivation on visual processing is enhanced spatial attention, in particular to the visual periphery and to moving stimuli. However, there is a parallel literature that has reported deficits in temporal aspects of visual processing in individuals with profound hearing losses. This study builds upon previous work showing possible deficits in processing of rapid serial visual presentation streams in deaf children [Restorative Neurology and Neuroscience (2010), 28, 181-192]. Deaf native signers of American Sign Language and hearing children and adults were asked to perform a 2-AFC identification task with a visual target embedded in a stream of visual stimuli presented at 6. Hz. Both children and adults displayed attentional awakening, whereby target identification accuracy improved as the number of stimuli preceding the target increased. For deaf children, however, this awakening effect was less pronounced than that observed in hearing children, interpreted as difficulty sustaining entrainment to the stimulus stream. The data provide the first account of attentional awakening in children, showing that it improves across the 6-13. year age range. They also provide additional support to the possibility of domain-general alterations in the processing of temporal information in the absence of auditory input. © 2014 Elsevier Ltd.


Simple DNA repeats (trinucleotide repeats, micro- and minisatellites) are prone to expansion/contraction via formation of secondary structures during DNA synthesis. Such structures both inhibit replication forks and create opportunities for template-primer slippage, making these repeats unstable. Certain aspects of simple repeat instability, however, suggest additional mechanisms of replication inhibition dependent on the primary DNA sequence, rather than on secondary structure formation. I argue that expanded simple repeats, due to their lower DNA complexity, should transiently inhibit DNA synthesis by locally depleting specific DNA precursors. Such transient inhibition would promote formation of secondary structures and would stabilize these structures, facilitating strand slippage. Thus, replication problems at simple repeats could be explained by potentiated toxicity, where the secondary structure-driven repeat instability is enhanced by DNA polymerase stalling at the low complexity template DNA. © 2013 WILEY Periodicals, Inc.


Chang H.-H.,University of Illinois at Urbana - Champaign
Psychometrika | Year: 2015

The paper provides a survey of 18 years' progress that my colleagues, students (both former and current) and I made in a prominent research area in Psychometrics-Computerized Adaptive Testing (CAT). We start with a historical review of the establishment of a large sample foundation for CAT. It is worth noting that the asymptotic results were derived under the framework of Martingale Theory, a very theoretical perspective of Probability Theory, which may seem unrelated to educational and psychological testing. In addition, we address a number of issues that emerged from large scale implementation and show that how theoretical works can be helpful to solve the problems. Finally, we propose that CAT technology can be very useful to support individualized instruction on a mass scale. We show that even paper and pencil based tests can be made adaptive to support classroom teaching.


Biswas R.R.,University of Illinois at Urbana - Champaign
Physical Review Letters | Year: 2013

We consider Majorana fermions tunneling among an array of vortices in a 2D chiral p-wave superconductor or equivalent material. The amplitude for Majorana fermions to tunnel between a pair of vortices is found to necessarily depend on the background superconducting phase profile; it is found to be proportional to the sine of half the difference between the phases at the two vortices. Using this result we study tight-binding models of Majorana fermions in vortices arranged in triangular or square lattices. In both cases we find that the aforementioned phase-tunneling relationship leads to the creation of superlattices where the Majorana fermions form macroscopically degenerate localizable flat bands at zero energy, in addition to other dispersive bands. This finding suggests that tunneling processes in these vortex arrays do not change the energies of a finite fraction of Majorana fermions, contrary to previous expectation. The presence of flat Majorana bands, and hence less-than-expected decoherence in these vortex arrays, bodes well for the prospects of topological quantum computation with large numbers of Majorana states. © 2013 American Physical Society.


Dlott D.D.,University of Illinois at Urbana - Champaign
Annual Review of Physical Chemistry | Year: 2011

This review discusses new developments in shock compression science with a focus on molecular media. Some basic features of shock and detonation waves, nonlinear excitations that can produce extreme states of high temperature and high pressure, are described. Methods of generating and detecting shock waves are reviewed, especially those using tabletop lasers that can be interfaced with advanced molecular diagnostics. Newer compression methods such as shockless compression and precompression shock that generate states of cold dense molecular matter are discussed. Shock compression creates a metallic form of hydrogen, melts diamond, and makes water a superionic liquid with unique catalytic properties. Our understanding of detonations at the molecular level has improved a great deal as a result of advanced nonequilibrium molecular simulations. Experimental measurements of detailed molecular behavior behind a detonation front might be available soon using femtosecond lasers to produce nanoscale simulated detonation fronts. © 2011 by Annual Reviews. All rights reserved.


Nienhaus G.U.,Karlsruhe Institute of Technology | Nienhaus G.U.,University of Illinois at Urbana - Champaign
Angewandte Chemie - International Edition | Year: 2012

Like the battery bunny: The novel photoswitchable fluorescent protein rsEGFP can be cycled between its fluorescent and nonfluorescent states more than a thousand times and is, therefore, a superb marker for high-resolution RESOLFT imaging (RESOLFT=reversible saturable optical fluorescence transition) and data storage applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Mayerich D.,University of Illinois at Urbana - Champaign
BMC bioinformatics | Year: 2012

One of the major goals in biomedical image processing is accurate segmentation of networks embedded in volumetric data sets. Biological networks are composed of a meshwork of thin filaments that span large volumes of tissue. Examples of these structures include neurons and microvasculature, which can take the form of both hierarchical trees and fully connected networks, depending on the imaging modality and resolution. Network function depends on both the geometric structure and connectivity. Therefore, there is considerable demand for algorithms that segment biological networks embedded in three-dimensional data. While a large number of tracking and segmentation algorithms have been published, most of these do not generalize well across data sets. One of the major reasons for the lack of general-purpose algorithms is the limited availability of metrics that can be used to quantitatively compare their effectiveness against a pre-constructed ground-truth. In this paper, we propose a robust metric for measuring and visualizing the differences between network models. Our algorithm takes into account both geometry and connectivity to measure network similarity. These metrics are then mapped back onto an explicit model for visualization.


Wu X.L.,University of Illinois at Urbana - Champaign
BMC bioinformatics | Year: 2012

With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous amount of computational resource, which is not accessible for most research groups and medical personnel. We have developed a novel de novo assembly framework, called Tiger, which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems. Our method is also flexible to embed different assemblers for various types of target genomes. Using the sequence data from a human chromosome, our results show that Tiger can achieve much better NG50s, better genome coverage, and slightly higher errors, as compared to Velvet and SOAPdenovo, using modest amount of memory that are available in commodity computers today. Most state-of-the-art assemblers that can achieve relatively high assembly quality need excessive amount of computing resource (in particular, memory) that is not available to most researchers to achieve high quality results. Tiger provides the only known viable path to utilize NGS de novo assemblers that require more memory than that is present in available computers. Evaluation results demonstrate the feasibility of getting better quality results with low memory footprint and the scalability of using distributed commodity computers.


Stankovic M.S.,KTH Royal Institute of Technology | Stipanovic D.M.,University of Illinois at Urbana - Champaign
Automatica | Year: 2010

In this paper the extremum seeking algorithm with sinusoidal perturbations has been extended and modified in two ways: (a) the output of the system is corrupted with measurement noise; (b) the amplitudes of the perturbation signals, as well as the gain of the integrator block, are time varying and tend to zero at a pre-specified rate. Convergence to the extremal point, with probability one, has been proved. Also, as a consequence of being able to cope with a stochastic environment, it has been shown how the proposed algorithm can be applied to mobile sensors as a tool for achieving the optimal observation positions. The proposed algorithm has been illustrated through several simulations. © 2010 Elsevier Ltd. All rights reserved.


Bhargava R.,University of Illinois at Urbana - Champaign
Applied Spectroscopy | Year: 2012

Infrared (IR) spectroscopic imaging seemingly matured as a technology in the mid-2000s, with commercially successful instrumentation and reports in numerous applications. Recent developments, however, have transformed our understanding of the recorded data, provided capability for new instrumentation, and greatly enhanced the ability to extract more useful information in less time. These developments are summarized here in three broad areas- data recording, interpretation of recorded data, and information extraction-and their critical review is employed to project emerging trends. Overall, the convergence of selected components from hardware, theory, algorithms, and applications is one trend. Instead of similar, general-purpose instrumentation, another trend is likely to be diverse and applicationtargeted designs of instrumentation driven by emerging component technologies. The recent renaissance in both fundamental science and instrumentation will likely spur investigations at the confluence of conventional spectroscopic analyses and optical physics for improved data interpretation. While chemometrics has dominated data processing, a trend will likely lie in the development of signal processing algorithms to optimally extract spectral and spatial information prior to conventional chemometric analyses. Finally, the sum of these recent advances is likely to provide unprecedented capability in measurement and scientific insight, which will present new opportunities for the applied spectroscopist.


An R.,University of Illinois at Urbana - Champaign
Journal of Nutrition in Gerontology and Geriatrics | Year: 2015

This study examines the impact of a home-delivered meal program on daily energy and nutrient intakes using nationally representative data from the National Health and Nutrition Examination Survey 2003–2012 waves. First-difference estimator addressed selection bias by using within-individual variations in diet and service use status between two nonconsecutive 24-hour dietary recalls among 145 home-delivered meal service users. Service use was found to be associated with a net increase in daily intake of protein by 8.39 g, fiber 3.39 g, calcium 145.94 mg, copper 0.16 mg, magnesium 45.37 mg, potassium 317.39 mg, selenium 14.04 mcg, and sodium 327.52 mg; whereas the effects on daily intake of total energy, fat, and vitamin D were not statistically significant. Home-delivered meals improve nutrient intakes among participants, but currently the program may be too limited in scale and capacity to best capitalize its beneficial impact on healthy aging and health care cost containment at the national level. © 2015, Copyright © Taylor & Francis Group, LLC.


Dall'Anese E.,University of Minnesota | Zhu H.,University of Illinois at Urbana - Champaign | Giannakis G.B.,University of Minnesota
IEEE Transactions on Smart Grid | Year: 2013

Optimal power flow (OPF) is considered for microgrids, with the objective of minimizing either the power distribution losses, or, the cost of power drawn from the substation and supplied by distributed generation (DG) units, while effecting voltage regulation. The microgrid is unbalanced, due to unequal loads in each phase and non-equilateral conductor spacings on the distribution lines. Similar to OPF formulations for balanced systems, the considered OPF problem is nonconvex. Nevertheless, a semidefinite programming (SDP) relaxation technique is advocated to obtain a convex problem solvable in polynomial-time complexity. Enticingly, numerical tests demonstrate the ability of the proposed method to attain the globally optimal solution of the original nonconvex OPF. To ensure scalability with respect to the number of nodes, robustness to isolated communication outages, and data privacy and integrity, the proposed SDP is solved in a distributed fashion by resorting to the alternating direction method of multipliers. The resulting algorithm entails iterative message-passing among groups of consumers and guarantees faster convergence compared to competing alternatives. © 2010-2012 IEEE.


Xiang Y.K.,University of Illinois at Urbana - Champaign
Circulation Research | Year: 2011

Activation of adrenergic receptors (AR) represents the primary mechanism to increase cardiac performance under stress. Activated βAR couple to Gs protein, leading to adenylyl cyclase-dependent increases in secondary-messenger cyclic adenosine monophosphate (cAMP) to activate protein kinase A. The increased protein kinase A activities promote phosphorylation of diversified substrates, ranging from the receptor and its associated partners to proteins involved in increases in contractility and heart rate. Recent progress with live-cell imaging has drastically advanced our understanding of the βAR-induced cAMP and protein kinase A activities that are precisely regulated in a spatiotemporal fashion in highly differentiated myocytes. Several features stand out: membrane location of βAR and its associated complexes dictates the cellular compartmentalization of signaling; βAR agonist dose-dependent equilibrium between cAMP production and cAMP degradation shapes persistent increases in cAMP signals for sustained cardiac contraction response; and arrestin acts as an agonist dose-dependent master switch to promote cAMP diffusion and propagation into intracellular compartments by sequestrating phosphodiesterase isoforms associated with the βAR signaling cascades. These features and the underlying molecular mechanisms of dynamic regulation of βAR complexes with adenylyl cyclase and phosphodiesterase enzymes and the implication in heart failure are discussed. © 2011 American Heart Association, Inc.


Yuksel S.,Queens University | Basar T.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2011

We consider the problem of remotely controlling a continuous-time linear time-invariant system driven by Brownian motion process, when communication takes place over noisy memoryless discrete- or continuous-alphabet channels. What makes this class of remote control problems different from most of the previously studied models is the presence of noise in both the forward channel (connecting sensors to the controller) and the reverse channel (connecting the controller to the plant). For stability of the closed-loop system, we look for the existence of an invariant distribution for the state, for which we show that it is necessary that the entire control space and the state space be encoded, and that the reverse channel be at least as reliable as the forward channel. We obtain necessary conditions and sufficient conditions on the channels and the controllers for stabilizability. Using properties of the underlying sampled Markov chain, we show that under variable-length coding and some realistic channel conditions, stability can be achieved over discrete-alphabet channels even if the entire state and control spaces are to be encoded and the number of bits that can be transmitted per unit time is strictly bounded. For control over continuous-alphabet channels, however, a variable rate scheme is not necessary. We also show that memoryless policies are rate-efficient for Gaussian channels. © 2011 IEEE.


Gilbert I.,University of Illinois at Urbana - Champaign
Nature Physics | Year: 2014

Artificial spin ice comprises a class of frustrated arrays of interacting single-domain ferromagnetic nanostructures. Previous studies of artificial spin ice have focused on simple lattices based on natural frustrated materials. Here we experimentally examine artificial spin ice created on the shakti lattice, a structure that does not directly correspond to any known natural magnetic material. On the shakti lattice, none of the near-neighbour interactions is locally frustrated, but instead the lattice topology frustrates the interactions leading to a high degree of degeneracy. We demonstrate that the shakti system achieves a physical realization of the classic six-vertex model ground state. Furthermore, we observe that the mixed coordination of the shakti lattice leads to crystallization of effective magnetic charges and the screening of magnetic excitations, underscoring the importance of magnetic charge as the relevant degree of freedom in artificial spin ice and opening new possibilities for studies of its dynamics.


Viswanathan M.,University of Illinois at Urbana - Champaign
Journal of Product Innovation Management | Year: 2012

In recent years, market-based approaches have been proposed for the base of the pyramid (BoP). However, the literature offers little theoretical or practical guidelines for innovative product development for what are radically new market contexts for most businesses in advanced economies. Considering that product development is a fundamental activity in a market economy, and that much BoP consumer welfare potentially arises from innovative and affordable goods and services that can solve critical life needs, this is a substantial gap in knowledge. This paper attempts to address this gap by using an analysis of 13 year-long university projects on BoP-focused concept and prototype development conducted between 2006 and 2010. An inventory of research propositions is developed that identifies factors necessary for effective product development for BoP markets. Implications for new product development research and practice are discussed. © 2011 Product Development & Management Association.


Martin L.W.,University of Illinois at Urbana - Champaign | Ramesh R.,Lawrence Berkeley National Laboratory
Acta Materialia | Year: 2012

We review recent developments and advances in multiferroic and magnetoelectric heterostructures. Driven by the promise of new materials functionality (i.e. electric field control of ferromagnetism), extensive on-going research is focused on the search for and characterization of new multiferroic materials. In this review we develop a comprehensive overview of multiferroic materials, including details on the nature of order parameters and coupling in these materials, the scarcity of such materials in single phase form, routes to create and control the properties of these materials, and we finish by investigating such effects in a number of model materials and heterostructures. This includes an in-depth discussion of BiFeO 3, an investigation of recent advances in magnetoelectric materials, and an introduction to a variety of approaches by which one can achieve novel materials functionality. © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.


Silverman S.K.,University of Illinois at Urbana - Champaign
Trends in Biochemical Sciences | Year: 2016

The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual and practical advantages of DNA relative to proteins and RNA. Early studies focused on RNA-cleaving deoxyribozymes, and more recent experiments have expanded the breadth of catalytic DNA to many other reactions. Including modified nucleotides has the potential to widen the scope of DNA enzymes even further. Practical applications of deoxyribozymes include their use as sensors for metal ions and small molecules. Structural studies of deoxyribozymes are only now beginning; mechanistic experiments will surely follow. Following the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines. As a synthetic catalyst identified by in vitro selection, single-stranded DNA has many advantages over proteins and RNA. The growing reaction scope of deoxyribozymes is increasing our fundamental understanding of biocatalysis, enabling applications in chemistry and biology.Including modified DNA nucleotides enhances the catalytic ability of deoxyribozymes. Several approaches for this purpose are being evaluated.Investigators are pursuing practical applications for deoxyribozymes, such as in vivo mRNA cleavage and sensing of metal ions and small molecules.High-resolution structural analysis of deoxyribozymes is a new field; the first crystal structure was recently reported. This structure provides an understanding of how DNA can be as catalytically competent as RNA. Structural information will enable mechanistic studies of deoxyribozymes. © 2016 Elsevier Ltd.


Wild A.L.,University of Illinois at Urbana - Champaign
PloS one | Year: 2013

Biological characters can be employed for both taxonomy and phylogenetics, but is conscripting characters for double duty a good idea? We explore the evolution of characters designed for taxonomic diagnosis in Costa Rican heterospiline wasps, a hyperdiverse lineage of parasitoid Braconidae, by mapping them to a robust multi-locus molecular phylogeny. We discover a strong positive relationship between the amount of evolutionary change a character undergoes and how broadly useful the characters are in the context of an interactive identification key--e.g., how evenly the character states are distributed among taxa. The empirical finding that fast characters are the most useful for species identification supports the idea that characters designed for taxonomic diagnoses are likely to underperform--or be positively misleading--in phylogenetic analyses.


Saini S.,University of Illinois at Urbana - Champaign
PLoS pathogens | Year: 2010

Salmonella enterica serovar Typhimurium is a common food-borne pathogen that induces inflammatory diarrhea and invades intestinal epithelial cells using a type three secretion system (T3SS) encoded within Salmonella pathogenicity island 1 (SPI1). The genes encoding the SPI1 T3SS are tightly regulated by a network of interacting transcriptional regulators involving three coupled positive feedback loops. While the core architecture of the SPI1 gene circuit has been determined, the relative roles of these interacting regulators and associated feedback loops are still unknown. To determine the function of this circuit, we measured gene expression dynamics at both population and single-cell resolution in a number of SPI1 regulatory mutants. Using these data, we constructed a mathematical model of the SPI1 gene circuit. Analysis of the model predicted that the circuit serves two functions. The first is to place a threshold on SPI1 activation, ensuring that the genes encoding the T3SS are expressed only in response to the appropriate combination of environmental and cellular cues. The second is to amplify SPI1 gene expression. To experimentally test these predictions, we rewired the SPI1 genetic circuit by changing its regulatory architecture. This enabled us to directly test our predictions regarding the function of the circuit by varying the strength and dynamics of the activating signal. Collectively, our experimental and computational results enable us to deconstruct this complex circuit and determine the role of its individual components in regulating SPI1 gene expression dynamics.


Liu L.,University of Illinois at Urbana - Champaign
Nature Geoscience | Year: 2014

In ancient orogens, such as the Appalachian Mountains in the eastern United States, the difference between the high and low points - topographic relief - can continue to increase long after the tectonic forces that created the range have become inactive. Climatic forcing and mantle-induced dynamic uplift could drive formation of relief, but clear evidence is lacking in the Appalachian Mountains. Here I use a numerical simulation of dynamic topography in North America, combined with reconstructions of the sedimentation history from the Gulf of Mexico, to show that rejuvenation of topographic relief in the Appalachian Mountains since the Palaeogene period could have been caused by mantle-induced dynamic subsidence associated with sinking of the subducted Farallon slab. Specifically, I show that patterns of continental erosion and the eastward migration of sediment deposition centres in the Gulf of Mexico closely follow the locus of predicted dynamic subsidence. Furthermore, pulses of rapid sediment deposition in the Gulf of Mexico and western Atlantic correlate with enhanced erosion in the Appalachian Mountains during the Miocene epoch, caused by dynamic tilting of the continent. The model predicts that such subsidence-induced differential erosion caused flexural-isostatic adjustments of Appalachian topography that led to the development of 400 m of relief and more than 200 m of elevation. I propose that dynamically induced continental tilting may provide a mechanism for topographic rejuvenation in ancient orogens. © 2014 Macmillan Publishers Limited.


Liu L.,University of Illinois at Urbana - Champaign
Geophysical Research Letters | Year: 2014

Interpretation of recent mantle seismic images below the America ignited a debate on the Cretaceous subduction polarity in the eastern Pacific Ocean. The traditional view is that the massive vertical slab wall under eastern North America resulted from an eastward Farallon subduction. An alternative interpretation attributes this prominent seismic structure to a westward subduction of the North American Plate against a stationary intraoceanic trench. Here I design quantitative subduction models to test these two scenarios, using their implied plate kinematics as velocity boundary conditions. Modeling results suggest that the westward subduction scenario could not produce enough slab volume as seismic images reveal, as is due to the overall slow subduction rate (~2.5 cm/yr). The results favor the continuous eastward Farallon subduction scenario, which, with an average convergence rate of >10 cm/yr prior to the Eocene, can properly generate both the volume and the geometry of the imaged lower mantle slab pile. The eastward subduction model is also consistent with most Cretaceous geological records along the west coast of North America. © 2014. American Geophysical Union. All Rights Reserved.


Wang Z.,University of Illinois at Urbana - Champaign
Journal of the Atmospheric Sciences | Year: 2014

The role of cumulus congestus (shallow and congestus convection) in tropical cyclone (TC) formation is examined in a high-resolution simulation of Tropical Cyclone Fay (2008). It is found that cumulus congestus plays a dominant role in moistening the lower to middle troposphere and spinning up the near-surface circulation prior to genesis, while deep convection plays a key role in moistening the upper troposphere and intensifying the cyclonic circulation over a deep layer. The transition from the tropical wave stage to the TC stage is marked by a substantial increase in net condensation and potential vorticity generation by deep convection in the inner wave pouch region. This study suggests that TC formation can be regarded as a two-stage process. The first stage is a gradual process of moisture preconditioning and low-level spinup, in which cumulus congestus plays a dominant role. The second stage commences with the rapid development of deep convection in the inner pouch region after the air column is moistened sufficiently, whereupon the concentrated convective heating near the pouch center strengthens the transverse circulation and leads to the amplification of the cyclonic circulation over a deep layer. The rapid development of deep convection can be explained by the power-law increase of precipitation rate with column water vapor (CWV) above a critical value. The high CWV near the pouch center thus plays an important role in convective organization. It is also shown that cumulus congestus can effectively drive the low-level convergence and provides a direct and simple pathway for the development of the TC protovortex near the surface. © 2014 American Meteorological Society.


Londergan J.T.,Indiana University Bloomington | Peng J.C.,University of Illinois at Urbana - Champaign | Thomas A.W.,Jefferson Lab | Thomas A.W.,University of Adelaide
Reviews of Modern Physics | Year: 2010

This review article discusses the experimental and theoretical status of partonic charge symmetry. It is shown how the partonic content of various structure functions gets redefined when the assumption of charge symmetry is relaxed. Various theoretical and phenomenological models for charge-symmetry violation in parton distribution functions are reviewed. After summarizing the current experimental upper limits on charge-symmetry violation in parton distributions, a series of new experiments are proposed, which might reveal partonic charge-symmetry violation or alternatively might lower the current upper limits on parton charge-symmetry violation. © 2010 The American Physical Society.


Chang W.-C.,Academia Sinica, Taiwan | Peng J.-C.,University of Illinois at Urbana - Champaign
Progress in Particle and Nuclear Physics | Year: 2014

We review the current status and future prospects on the subject of flavor structure of the nucleon sea. The flavor structure of the nucleon sea provides unique information on the non-perturbative aspects of strong interactions allowing stringent tests of various models on the partonic structures of the nucleons as well as lattice QCD calculations. The scope of this review covers the unpolarized, polarized, and the transverse-momentum dependent sea-quark distributions of the nucleons. While the main focus of this review is on the physics motivation and recent progress on the subject of the nucleon sea, we also discuss future prospects of addressing some outstanding issues on the flavor structure of the nucleon sea. © 2014 Elsevier Ltd. All rights reserved.


Willenbrock S.,University of Illinois at Urbana - Champaign | Willenbrock S.,Fermi National Accelerator Laboratory | Zhang C.,Catholic University of Louvain
Annual Review of Nuclear and Particle Science | Year: 2014

We review the effective field theory approach to physics beyond the Standard Model using dimension-six operators. Topics include the choice of operator basis, electroweak boson pair production, precision electroweak physics (including one-loop contributions), and Higgs physics. By measuring the coefficients of dimension-six operators with good accuracy, we can hope to infer some or all of the features of the theory that lies beyond the Standard Model. Copyright © 2014 by Annual Reviews. All rights reserved.


Saini S.,University of Illinois at Urbana - Champaign
PLoS pathogens | Year: 2010

Salmonella enterica serovar Typhimurium is a common food-borne pathogen that induces inflammatory diarrhea and invades intestinal epithelial cells using a type three secretion system (T3SS) encoded within Salmonella pathogenicity island 1 (SPI1). The genes encoding the SPI1 T3SS are tightly regulated by a network of interacting transcriptional regulators involving three coupled positive feedback loops. While the core architecture of the SPI1 gene circuit has been determined, the relative roles of these interacting regulators and associated feedback loops are still unknown. To determine the function of this circuit, we measured gene expression dynamics at both population and single-cell resolution in a number of SPI1 regulatory mutants. Using these data, we constructed a mathematical model of the SPI1 gene circuit. Analysis of the model predicted that the circuit serves two functions. The first is to place a threshold on SPI1 activation, ensuring that the genes encoding the T3SS are expressed only in response to the appropriate combination of environmental and cellular cues. The second is to amplify SPI1 gene expression. To experimentally test these predictions, we rewired the SPI1 genetic circuit by changing its regulatory architecture. This enabled us to directly test our predictions regarding the function of the circuit by varying the strength and dynamics of the activating signal. Collectively, our experimental and computational results enable us to deconstruct this complex circuit and determine the role of its individual components in regulating SPI1 gene expression dynamics.


Granato A.V.,University of Illinois at Urbana - Champaign
Journal of Non-Crystalline Solids | Year: 2011

The non-Arrhenius Vogel-Fulcher-Tamman relation for the viscosity, η, known for about 8 decades, describes simply one of the most characteristic features of supercooled liquids. It may be written η=η0expU/kT-T0. Using the Dyre et al. result demonstrating that U is proportional to the shear modulus, G, and the Interstitialcy Theory of Condensed Matter (ITCM) we derive this relation and obtain T0/Tg=γ/γ+1 and U=U0/1+γ, where U 0 is the interstitialcy diffusion energy at the glass temperature. Here, γ is a fragility softening parameter given by γ = βT g(dc /dT)| Tg. β is the shear susceptibility - d ln G /dc, and c is the interstitialcy concentration. γ is also a fragility parameter ranging from 0 for strong materials to 3 or above for fragile ones. © 2010 Elsevier B.V.All rights reserved.


The statistics of convective processes and vertical vorticity from the tropical wave to tropical cyclone stage are examined in a high-resolution simulation of Tropical Cyclone Fay (2008). The intensity of vertical velocity follows approximately the truncated lognormal distribution in the model simulation, which is consistent with previous observational studies. The upward motion at the pregenesis stage is weaker compared to mature hurricanes or midlatitude thunderstorms. The relatively strong upward velocities occupying a small areal fraction make a substantial contribution to the upward mass and moisture fluxes and condensation. It is also found that upward motion and downward motion both intensify with time, but the former is stronger than the latter, and the mean vertical motion and the mean vertical mass flux thus increase with time. By contrast, the maximum anticyclonic vorticity is comparable to the maximum cyclonic vorticity in magnitude. Both cyclonic vorticity and anticyclonic vorticity intensify with time, but the former covers a larger areal fraction in the lower and middle troposphere and becomes dominant throughout the troposphere after genesis. Sensitivity tests with different model resolutions were carried out to test the robustness of the results. When the horizontal grid spacing is reduced, the size of updrafts decreases and the number of updrafts increases, but the areal fraction of updrafts, the mean vertical velocity, and the mean vertical mass flux are rather insensitive to themodel resolution, especially in the lower troposphere and when the model resolution is 1km or higher. This may explain why models with relatively coarse resolution can simulate tropical cyclogenesis reasonably well. © 2014 American Meteorological Society.


This paper performed a comparative analysis of organic Rankine cycle (ORC) using different working fluids, in order to recover waste heat from a solid oxide fuel cell-gas turbine hybrid power cycle. Depending on operating parameters, criteria for the choice of the working fluid were identified. Results reveal that due to a significant temperature glide of the exhaust gas, the actual ORC cycle thermal efficiency strongly depends on the turbine inlet temperature, exhaust gas temperature, and fluid's critical point temperature. When exhaust gas temperature varies in the range of 500K to 600K, R123 is preferred among the nine dry typical organic fluids because of the highest and most stabilized mean thermal efficiency under wide operating conditions and its reasonable condensing pressure and turbine outlet specific volume, which in turn results in a feasible ORC cycle for practical concerns. © 2012 John Wiley & Sons, Ltd.


Kral M.J.,University of Illinois at Urbana - Champaign
Medical Anthropology Quarterly | Year: 2013

Inuit youth suicide is at an epidemic level in the circumpolar north. Rapid culture change has left Inuit in a state of coloniality that destabilized their kin-based social organization, and in spite of advances in self-governance social problems such as suicide continue. Drawing on ethnographic fieldwork I carried out in Nunavut, Canada (2004-2005), including 27 interviews with Inuit between the ages of 17 and 61, I examine male youth in particular in the context of recent colonial change, gender ideologies and behavior, youth autonomy, and the family. Anger is common among Inuit male youth, often directed toward girlfriends and parents, and suicide is embedded in some of these relationships. Many Inuit male youth are struggling with a new cultural model of love and sexuality. Inuit speak about a need for more responsible parenting. Evidence is beginning to show, however, that local, community-based suicide prevention may be working. © 2013 by the American Anthropological Association.


Motl R.W.,University of Illinois at Urbana - Champaign
Physical Medicine and Rehabilitation Clinics of North America | Year: 2013

Walking impairment is a common consequence of multiple sclerosis (MS) that can result in substantial limitations of daily activities and compromised quality of life. Walking impairment is often monitored as an indicator of disease and neurologic disability progression. The worsening of walking performance while undertaking a cognitive task underscores the role of nonmotor impairments in ambulation limitations. Walking impairment has ubiquitous and life-altering consequences, underscoring the importance of continued efforts to identify approaches to prevent and forestall this event, and to restore walking ability in persons with MS. © 2013 Elsevier Inc.


Burkhardt Jr. R.W.,University of Illinois at Urbana - Champaign
Genetics | Year: 2013

Scientists are not always remembered for the ideas they cherished most. In the case of the French biologist Jean-Baptiste Lamarck, his name since the end of the nineteenth century has been tightly linked to the idea of the inheritance of acquired characters. This was indeed an idea that he endorsed, but he did not claim it as his own nor did he give it much thought. He took pride instead in advancing the ideas that (1) nature produced successively all the different forms of life on earth, and (2) environmentally induced behavioral changes lead the way in species change. This article surveys Lamarck's ideas about organic change, identifies several ironies with respect to how his name is commonly remembered, and suggests that some historical justice might be done by using the adjective "Lamarckian" to denote something more (or other) than a belief in the inheritance of acquired characters. © 2013 by the Genetics Society of America.


Lavalle S.M.,University of Illinois at Urbana - Champaign
IEEE Robotics and Automation Magazine | Year: 2011

This is the first installment of a two-part tutorial. The goal of the first part is to give the reader a basic understanding of the technical issues and types of approaches in solving the basic path-planning or obstacle-avoidance problem. The second installment will cover more advanced issues, including feedback, differential constraints, and uncertainty. Note that this is a brief tutorial rather than a comprehensive survey of methods. For the latter, consult some of the recent textbooks [4], [9]. © 2006 IEEE.


Irwin D.E.,University of Illinois at Urbana - Champaign
Memory | Year: 2014

The effect of eye blinks on short-term memory was examined in two experiments. On each trial, participants viewed an initial display of coloured, oriented lines, then after a retention interval they viewed a test display that was either identical or different by one feature. Participants kept their eyes open throughout the retention interval on some blocks of trials, whereas on others they made a single eye blink. Accuracy was measured as a function of the number of items in the display to determine the capacity of short-term memory on blink and no-blink trials. In separate blocks of trials participants were instructed to remember colour only, orientation only, or both colour and orientation. Eye blinks reduced short-term memory capacity by approximately 0.6–0.8 items for both feature and conjunction stimuli. A third, control, experiment showed that a button press during the retention interval had no effect on short-term memory capacity, indicating that the effect of an eye blink was not due to general motoric dual-task interference. Eye blinks might instead reduce short-term memory capacity by interfering with attention-based rehearsal processes. © 2013, © 2013 Taylor & Francis.


Tuchler M.,Rheinmetall AG | Singer A.C.,University of Illinois at Urbana - Champaign
IEEE Transactions on Information Theory | Year: 2011

Turbo codes and the iterative algorithm for decoding them sparked a new era in the theory and practice of error control codes. Turbo equalization followed as a natural extension to this development, as an iterative technique for detection and decoding of data that has been both protected with forward error correction and transmitted over a channel with intersymbol interference (ISI). In this paper, we review the turbo equalization approach to coded data transmission over ISI channels, with an emphasis on the basic ideas, some of the practical details, and many of the research directions that have arisen from this offshoot, introduced by Douillard, of the original turbo decoding algorithm. The subsequent relaxation of the maximum a posteriori (MAP) equalization algorithm to include linear and other simpler receivers sparked a decade and a half of research into iterative algorithms, spanning research problems ranging from trellis coded modulation to underwater acoustic communications. © 2006 IEEE.


Wilson B.,University of Illinois at Urbana - Champaign
Landscape and Urban Planning | Year: 2013

This study uses a unique dataset to examine the relationship between residential electricity consumption and subdivision design characteristics, while controlling for a range of important covariates. Households in three Illinois counties completed a mail survey regarding energy consumption and also signed a waiver allowing the local utility to provide their electricity consumption records for the previous 12 month period. Summer, winter, and annual electricity consumption was modeled as a function of climate, demographic, structural, technological, behavioral, and urban form factors using linear regression. Hypothesized interactions between urban form characteristics and climate factors were tested and interpreted graphically. The most consistent predictors of household electricity usage are climate days, household size, number of bedrooms, and heating equipment. The negative relationship observed between net density at the subdivision level and summer electricity usage is consistent with arguments in favor of more compact development patterns and is interpreted in the context of the heat island effect. Edge contrast is also an important factor in understanding winter electricity use with wind shielding as the underlying explanatory mechanism. Homes in subdivisions that are more compact and less peripheral are likely to reap benefits in the form of reduced electricity consumption. © 2013 Elsevier B.V.


Chassy B.M.,University of Illinois at Urbana - Champaign
Regulatory Toxicology and Pharmacology | Year: 2010

Omic technologies can in principle allow visualization of the all of changes that take place when the genetics, nutrition or environment of an organism is altered. Targeted compositional analysis is today a key component of the food safety assessment paradigm in which known nutrients, anti-nutrients, toxicants, allergens, and other molecules of potential biological importance to humans or animals are quantitatively analyzed. This allows safety assessors to compare the composition and safety of one food with closely related counterparts. Omic technologies measure many analytes-some of which are unidentified-but the analysis often sacrifices one or more of the characteristics of validated analytical methods currently used for food analysis. Databases that would allow the safety assessor to interpret differences are not currently available. There is also no reason to believe that the targeted compositional analysis in use today does not provide the evidence needed to ensure food safety, nor is there any current reason to believe that omics can add value to the safety assessment process. The regulation of transgenic crops is far more rigorous than is justified since they present no new risks compared with traditional breeding, and are more precisely defined and better understood than their non-transgenic equivalent. © 2010 Elsevier Inc.


Chakrabarti R.,University of Illinois at Urbana - Champaign
Social Science and Medicine | Year: 2010

The aim of this paper is to elucidate the links between place and Bengali immigrant women's use of social networks in their efforts to live a healthy pregnancy. The literature on therapeutic landscapes has mostly emphasized characteristics of local places. I argue that social networks constituted in and beyond the places where people live are equally important. I draw on findings of a qualitative study conducted with Bengali immigrant women in New York City between 2004 and 2006 to understand the place-creating characteristics of social therapeutic networks. In-depth interviews with 40 women in selected neighborhoods in New York City show that such networks operated at multiple scales, ranging from the local to the transnational. A mix of tangible and virtual care and support were received through face-to face interaction and phone conversations. Advice on how to live a healthy pregnancy, cooking and bringing or sending food and therapeutic conversations emerged as important kinds of care and support provided by therapeutic networks. These networks worked in complex ways, reflecting: 1) the situational context of women's lives, shaped by the temporal (e.g. length of residence) and place-based (e.g. residential geographies) aspects of migration, 2) the importance of 'imaginative aspects' in shaping the meanings women formed of therapeutic networks and 3) the diverse ways in which women created and sustained these networks, based on class, country of origin, religion and culture. © 2010 Elsevier Ltd.


Akresh R.,University of Illinois at Urbana - Champaign
Future of Children | Year: 2016

We have good reason to predict that a warming climate will produce more conflict and violence. A growing contingent of researchers has been examining the relationship in recent years, and they’ve found that hotter temperatures and reduced rainfall are linked to increases in conflict at all scales, from interpersonal violence to war. Children are especially vulnerable to conflict, Richard Akresh writes. In addition to directly exposing children to violence and trauma, conflict can tear families apart, displace whole populations, interrupt schooling, cut off access to health care or food, and eliminate the jobs that families depend on for a living. Children caught in a war zone may suffer physical injuries, malnutrition, developmental delays, and psychological damage, with effects on their physical health, mental health, and education that can persist into adulthood and constrict their ability to make a living. Moreover, those effects can spill over to the next generation and beyond, damaging the affected countries’ ability to develop human capital. The likelihood that rates of conflict will increase on a hotter planet, then, poses a serious threat to children’s wellbeing—especially in poorer countries, which already see the most wars and other conflicts. Unfortunately, Akresh writes, we still poorly understand the mechanisms that link climate to conflict, and we have almost no evidence to tell us which types of policies could best mitigate the effects of climate change-related violence on children. © 2016, Center for the Future of Children. All rights reserved.


Pop E.,University of Illinois at Urbana - Champaign
Nano Research | Year: 2010

Understanding energy dissipation and transport in nanoscale structures is of great importance for the design of energy-efficient circuits and energy-conversion systems. This is also a rich domain for fundamental discoveries at the intersection of electron, lattice (phonon), and optical (photon) interactions. This review presents recent progress in understanding and manipulation of energy dissipation and transport in nanoscale solid-state structures. First, the landscape of power usage from nanoscale transistors (~10-8 W) to massive data centers (~109 W) is surveyed. Then, focus is given to energy dissipation in nanoscale circuits, silicon transistors, carbon nanostructures, and semiconductor nanowires. Concepts of steady-state and transient thermal transport are also reviewed in the context of nanoscale devices with sub-nanosecond switching times. Finally, recent directions regarding energy transport are reviewed, including electrical and thermal conductivity of nanostructures, thermal rectification, and the role of ubiquitous material interfaces. © 2010 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.


Bogg T.,Wayne State University | Roberts B.W.,University of Illinois at Urbana - Champaign
Annals of Behavioral Medicine | Year: 2013

Purpose: Recent initiatives by major funding agencies have emphasized translational and personalized approaches (e.g., genetic testing) to health research and health management. While such directives are appropriate, and will likely produce tangible health benefits, we seek to highlight a confluence of several lines of research showing relations between the personality dimension of conscientiousness and a variety of health-related outcomes. Methods: Using a modified health process model, we review the compelling evidence linking conscientiousness to health and disease processes, including longevity, diseases, morbidity-related risk factors, health-related psychophysiological mechanisms, health-related behaviors, and social environmental factors related to health. Conclusion: We argue the accumulated evidence supports greater integration of conscientiousness into public health, epidemiological, and medical research, with the ultimate aim of understanding how facilitating more optimal trait standing might foster better health. © 2012 The Society of Behavioral Medicine.


Tappenden K.A.,University of Illinois at Urbana - Champaign
Archives of Surgery | Year: 2010

Given the immeasurable human distress and health care burden associated with intestinal failure, medical therapies aimed at intestinal rehabilitation are needed. Following massive small-bowel resection, the residual intestine is known to adapt structurally and functionally in an attempt to compensate for the resected portion. However, parenteral nutrition may be associated with many short- and long-term complications, including prevention of intestinal adaptation and promotion of mucosal atrophy due to lack of stimulus provided by oral or enteral nutrition. However, data herein demonstrate that the addition of butyrate, a short-chain fatty acid produced in the colon by dietary fiber fermentation, stimulates intestinal adaptation when added to parenteral nutrition, indicating that current solutions could be formulated to optimize intestinal adaptation and to reduce dependence of individuals with intestinal failure receiving long-term parenteral nutrition regimens. ©2010 American Medical Association. All rights reserved.


You H.,Xian Jiaotong University | Yang S.,Xian Jiaotong University | Ding B.,Xian Jiaotong University | Yang H.,University of Illinois at Urbana - Champaign
Chemical Society Reviews | Year: 2013

This Review is focused on the recent progresses in the synthetic approaches to the precise control of structure, size, shape, composition and multi-functionality of metal and metal alloy nanoparticles. Many of these strategies have been developed based on colloidal methods, and to limited extent, the galvanic and other methods. The shape, size and composition often govern the chemical and catalytic properties that are important for electrochemical energy applications. The structure-property relationship and the design in controllable structures and morphologies for specific reactions such as oxygen reduction reaction (ORR) are emphasized. © 2013 The Royal Society of Chemistry.


Knox R.V.,University of Illinois at Urbana - Champaign
Reproduction in Domestic Animals | Year: 2011

Contents: Opportunities for use of frozen-thawed semen (FTS) must address genetic advancement and fertility for developing practical models for use. Concerns about slowed genetic gains, lowered fertility and additional costs may limit use of FTS. However, FTS is presently used for international exchange among nucleus farms to help maintain genetic diversity. Use of FTS beyond several days can provide increased flexibility for on-farm use and allow additional time for disease tests. There may be potential for use of FTS for short-term banking during periods of low demand and while sires await breeding value tests. Opportunities exist for FTS use in long-term banking of sire lines, creation of semen pools for genetic progress evaluation and for use in emergencies. Advancing FTS technology will require the following: (i) more efficient production of doses; (ii) improved fertility with single sire or pooled matings; (iii) education and training; and (iv) models for FTS use and economics for use under various scenarios. © 2011 Blackwell Verlag GmbH.


Zhang X.-B.,Hunan University | Kong R.-M.,Hunan University | Lu Y.,University of Illinois at Urbana - Champaign
Annual Review of Analytical Chemistry | Year: 2011

Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb2+, Cu2+, Hg2+, and UO22+. In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes. Copyright © 2011 by Annual Reviews. All rights reserved.


Beutner G.L.,Bristol Myers Squibb | Denmark S.E.,University of Illinois at Urbana - Champaign
Angewandte Chemie - International Edition | Year: 2013

Since the landmark publications of the first directed aldol addition reaction in 1973, the site, diastereo-, and enantioselective aldol reaction has been elevated to the rarefied status of being both a named and a strategy-level reaction (the Mukaiyama directed aldol reaction). The importance of this reaction in the stereoselective synthesis of untold numbers of organic compounds, both natural and unnatural, cannot be overstated. However, its impact on the field extends beyond the impressive applications in synthesis. The directed aldol reaction has served as a fertile proving ground for new concepts and new methods for stereocontrol and catalysis. This Minireview provides a case history of how the challenges of merging site selectivity, diastereoselectivity, enantioselectivity, and catalysis into a unified reaction manifold stimulated the development of Lewis base catalyzed aldol addition reactions. The evolution of this process is chronicled from the authors' laboratories as well as in those of Professor Teruaki Mukaiyama. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


This paper describes the impacts of Neolithic Period (c. 5000-3200 cal. BP) and Iron Age (c. 3200-2300 cal. BP) occupation and land use on the geomorphology of residual hills that punctuate an expansive planation surface in central Karnataka, South India. Analyses of archaeological survey data, soil and regolith profiles, remotely sensed metrics of hill morphology and distributions of soil and sediment, and paleoecological data indicate that cultural land use altered the morphology of these features and the distribution of soils on them, and consequently impacted the processes by which they continued to develop. Statistical regression models indicate that archaeological evidence for ancient land use is a significant explanatory variable for the proportion of remaining soil cover and exposed residual rock on the sampled hills. Moreover, multivariate regression models explaining soil removal on the hills are effective when including archaeological proxies for ancient land use along with other geomorphological variables. The combined effects of intensified agro-pastoral land use, vegetation changes, and variations in climatic humidity during the mid-Holocene to late Holocene appear to have facilitated erosional conditions that outpaced subsurface weathering. These findings imply that the refinement of models for the development of residual hills in South India, where early paradigms for explaining the evolution of such landforms were formalized, should consider the effects of Holocene land use where applicable. The findings also suggest that recent efforts to understand the unique ecology of these landforms should account for historical human land use. © The Author(s) 2013.


Olson K.R.,University of Illinois at Urbana - Champaign
Geoderma | Year: 2013

The atmospheric levels of carbon dioxide (CO2) have been due largely to the burning of fossil fuels, deforestation, cultivation of the grasslands, drainage of the land, and land use changes. This has led to increase in greenhouse gases, created concerns about the potential for long-term climate change and interest in developing methods to sequester some of this atmospheric carbon. In agricultural land areas no-tillage (NT) systems have been proposed, to replace moldboard plow and chisel systems as a way to sequester soil organic carbon (SOC). Numerous estimates have been published of soil organic carbon (SOC) sequestration total and rates as a result of a switch to NT systems. Other researchers have proposed the use of cover crops, synthetic fertilizers, organic fertilizer, manure, liming, agricultural systems and management, agroforestry, forages, compost, crop rotations, and reduced row crop use as ways to sequester SOC. For SOC sequestration to occur as a result of a treatment applied to a land unit, all of the SOC sequestered must have come from atmosphere and be transferred into the soil humus through the unit plants, plant residues and other organic solids. The amount of SOC present in the soil humus at the end of the study has to be greater than the pre-treatment SOC levels in the same land unit and there needs to be a net depletion of atmospheric CO2 as a result. The objectives of this paper are to: (1) determine long-term study SOC levels and trends in agricultural lands, (2) application of the SOC sequestration concept to a specific site, (3) identify appropriate experimental designs for plot area use in determining SOC sequestration, (4) develop a procedure, such as pre-treatment measurements of SOC levels in the plots before treatments are applied, to verify SOC sequestration at a site (5) equivalent soil mass sampling method, (6) compare laboratory methods for quantifying SOC content, and (7) account for the loading of C rich amendments. To unequivocally demonstrate SOC sequestration at a specific site has occurred, a temporal increase must be documented relative to pre-treatment SOC level and linked to a net depletion of atmospheric CO2. © 2012.


Shogren K.A.,University of Illinois at Urbana - Champaign
Intellectual and Developmental Disabilities | Year: 2013

In light of the rapid evolution of research, policy, and practice in the intellectual disability (ID) field resulting from shifts in our conceptualization of disability and in frameworks for the diagnosis and classification of ID, systematic consideration of the multiple, interrelated contextual factors that impact research, policy, and practice are necessary to achieve valued outcomes for individuals with disabilities, their families, and society. The purpose of this article is to introduce a recently developed consensus definition of context and elaborate on application of this definition to research, practice, and policy in the ID field, with a specific focus on how context may be able to serve as an integrative concept to support the attainment of valued outcomes in the disability field for individuals with disabilities, their families, and society. © AAIDD.


Benjamin A.S.,University of Illinois at Urbana - Champaign
Psychology and Aging | Year: 2016

How do we best characterize the memory deficits that accompany aging? A popular hypothesis, articulated originally by Naveh-Benjamin (2000) and reviewed in the accompanying article by Smyth and Naveh-Benjamin (2016), suggests that older adults are selectively deficient in establishing associations between to-be-learned memoranda and as a result have deficits in memory for sources or contexts. An alternative proposal, called density of representations yields age-related deficits (DRYAD) and outlined in recent articles by Benjamin (2010) and colleagues (Benjamin, Diaz, Matzen, & Johnson, 2012), attributes disproportionate deficits in memory to a global, rather than a selective, deficit of memory. In an attempt to adjudicate between these competing positions, Smyth and Naveh-Benjamin (2016) discussed 2 sets of experimental data that they claim speak against the global deficit model. Here I review some general principles of how the global-deficit view is applied to experimental paradigms and demonstrate that even a simplified form of DRYAD can comfortably accommodate the critical findings cited by Smyth and Naveh-Benjamin. I also evaluate aspects of their results that may be problematic for DRYAD and describe ways in which DRYAD's account of associative recognition can be falsified. I end with a discussion of the complementary strengths and weaknesses of the 2 approaches and consider ways in which the associative deficit hypothesis and DRYAD might work more profitably together than apart. © 2015 American Psychological Association.


Kwan M.-P.,University of Illinois at Urbana - Champaign
Annals of the Association of American Geographers | Year: 2013

Many fundamental notions in geographic and social science research still tend to be conceptualized largely in static spatial terms, ignoring how our understanding of the issues we study can be greatly enriched through the lenses of time and human mobility. This article revisits three such notions: racial segregation, environmental exposure, and accessibility. It argues for the need to expand our analytical focus from static residential spaces to other relevant places and times in people's everyday lives. Mobility is an essential element of people's spatiotemporal experiences, and these complex experiences cannot be fully understood by just looking at where people live. As many social scientists are interested in studying segregation, environmental exposure, and accessibility, geographers can contribute to advancing temporally integrated analysis of these issues through careful examination of people's everyday experiences as their lives unfold in space and time. Interdisciplinary research along this line could have a broad impact on many disciplines beyond geography. © 2013 Copyright Taylor and Francis Group, LLC.


Kemper J.K.,University of Illinois at Urbana - Champaign
Biochimica et Biophysica Acta - Molecular Basis of Disease | Year: 2011

Abnormally elevated lipid and glucose levels due to the disruption of metabolic homeostasis play causative roles in the development of metabolic diseases. A cluster of metabolic conditions, including dyslipidemia, abdominal obesity, and insulin resistance, is referred to as metabolic syndrome, which has been increasing globally at an alarming rate. The primary nuclear bile acid receptor, Farnesoid X Receptor (FXR, NR1H4), plays important roles in controlling lipid and glucose levels by regulating expression of target genes in response to bile acid signaling in enterohepatic tissues. In this review, I discuss how signal-dependent FXR transcriptional activity is dynamically regulated under normal physiological conditions and how it is dysregulated in metabolic disease states. I focus on the emerging roles of post-translational modifications (PTMs) and transcriptional cofactors in modulating FXR transcriptional activity and pathways. Dysregulation of nuclear receptor transcriptional signaling due to aberrant PTMs and cofactor interactions are key determinants in the development of metabolic diseases. Therefore, targeting such abnormal PTMs and transcriptional cofactors of FXR in disease states may provide a new molecular strategy for development of pharmacological agents to treat metabolic syndrome. This article is part of a Special Issue entitled: Translating nuclear receptors from health to disease. © 2010 Elsevier B.V.


Abbas A.E.,University of Illinois at Urbana - Champaign
Operations Research | Year: 2013

The construction of a multiattribute utility function is an important step in decision analysis and can be a challenging task unless some decomposition of the utility function is performed. When every attribute is utility independent of its complement, the utility elicitation task is significantly simplified because the functional form of the utility function requires only one conditional utility function for each attribute, and some normalizing constants. When utility independence conditions do not hold, the conditional utility function of an attribute may vary across the domain of the complement attributes, and therefore a single conditional utility assessment for each attribute may not be sufficient to capture the decision maker's preferences. This paper proposes a method to construct utility functions that have the flexibility to match the variations in the conditional utility function, across the domain of the attributes, using univariate utility assessments at the boundary values. The approach incorporates the boundary assessments into a new function, which we call the double-sided utility copula. This formulation provides a wealth of new functional forms that the analyst may use to incorporate utility dependence in multiattribute decision problems. The utility copula function also allows for the flexibility to incorporate a wide range of trade-off assessments among the attributes, while keeping the utility assessments at the boundary values fixed. It is also useful in determining the order of approximation provided by using certain independence assumptions in a multiattribute decision problem when the attributes are utility dependent. © 2013 INFORMS.


LaValle S.M.,University of Illinois at Urbana - Champaign
IEEE Robotics and Automation Magazine | Year: 2011

Here, we give the Part II of the two-part tutorial. Part I emphasized the basic problem formulation, mathematical concepts, and the most common solutions. The goal of Part II is to help you understand current robotics challenges from a motionplanning perspective. © 2011 IEEE.


Freund J.B.,University of Illinois at Urbana - Champaign
Journal of Sound and Vibration | Year: 2011

Advanced simulation tools, particularly large-eddy simulation techniques, are becoming capable of making quality predictions of jet noise for realistic nozzle geometries and at engineering relevant flow conditions. Increasing computer resources will be a key factor in improving these predictions still further. Quality prediction, however, is only a necessary condition for the use of such simulations in design optimization. Predictions do not themselves lead to quieter designs. They must be interpreted or harnessed in some way that leads to design improvements. As yet, such simulations have not yielded any simplifying principals that offer general design guidance. The turbulence mechanisms leading to jet noise remain poorly described in their complexity. In this light, we have implemented and demonstrated an aeroacoustic adjoint-based optimization technique that automatically calculates gradients that point the direction in which to adjust controls in order to improve designs. This is done with only a single flow solutions and a solution of an adjoint system, which is solved at computational cost comparable to that for the flow. Optimization requires iterations, but having the gradient information provided via the adjoint accelerates convergence in a manner that is insensitive to the number of parameters to be optimized. This paper, which follows from a presentation at the 2010 IUTAM Symposium on Computational Aero-Acoustics for Aircraft Noise Prediction, reviews recent and ongoing efforts by the author and co-workers. It provides a new formulation of the basic approach and demonstrates the approach on a series of model flows, culminating with a preliminary result for a turbulent jet. © 2011 Elsevier Ltd.


Wang X.,University of Illinois at Urbana - Champaign | Lemmon M.D.,University of Notre Dame
IEEE Transactions on Automatic Control | Year: 2011

This paper examines event-triggered data transmission in distributed networked control systems with packet loss and transmission delays. We propose a distributed event-triggering scheme, where a subsystem broadcasts its state information to its neighbors only when the subsystem's local state error exceeds a specified threshold. In this scheme, a subsystem is able to make broadcast decisions using its locally sampled data. It can also locally predict the maximal allowable number of successive data dropouts (MANSD) and the state-based deadlines for transmission delays. Moreover, the designer's selection of the local event for a subsystem only requires information on that individual subsystem. Our analysis applies to both linear and nonlinear subsystems. Designing local events for a nonlinear subsystem requires us to find a controller that ensures that subsystem to be input-to-state stable. For linear subsystems, the design problem becomes a linear matrix inequality feasibility problem. With the assumption that the number of each subsystem's successive data dropouts is less than its MANSD, we show that if the transmission delays are zero, the resulting system is finite-gain ℒ p stable. If the delays are bounded by given deadlines, the system is asymptotically stable. We also show that those state-based deadlines for transmission delays are always greater than a positive constant. © 2006 IEEE.


Martin L.W.,University of Illinois at Urbana - Champaign
Dalton Transactions | Year: 2010

An in-depth look at the complex materials chemistry of multiferroics is undertaken. In the last decade, considerable attention has been focused on the search for and characterization of new multiferroic materials as scientists and researchers have been driven by the promise of exotic materials functionality (i.e., electric field control of ferromagnetism). In this manuscript we develop a picture of multiferroic materials, including details on the nature of order parameters and coupling in these materials, the scarcity of such materials, routes to create and control the properties in these materials, and we finish by investigating such effects in the model multiferroic BiFeO3. © The Royal Society of Chemistry 2010.


Sturm R.,RAND Corporation | An R.,University of Illinois at Urbana - Champaign
CA Cancer Journal for Clinicians | Year: 2014

This review summarizes current understanding of economic factors during the obesity epidemic and dispels some widely held, but incorrect, beliefs. Rising obesity rates coincided with increases in leisure time (rather than increased work hours), increased fruit and vegetable availability (rather than a decline in healthier foods), and increased exercise uptake. As a share of disposable income, Americans now have the cheapest food available in history, which fueled the obesity epidemic. Weight gain was surprisingly similar across sociodemographic groups or geographic areas, rather than specific to some groups (at every point in time; however, there are clear disparities). It suggests that if one wants to understand the role of the environment in the obesity epidemic, one needs to understand changes over time affecting all groups, not differences between subgroups at a given time. Although economic and technological changes in the environment drove the obesity epidemic, the evidence for effective economic policies to prevent obesity remains limited. Taxes on foods with low nutritional value could nudge behavior toward healthier diets, as could subsidies/discounts for healthier foods. However, even a large price change for healthy foods could close only part of the gap between dietary guidelines and actual food consumption. Political support has been lacking for even moderate price interventions in the United States and this may continue until the role of environmental factors is accepted more widely. As opinion leaders, clinicians play an important role in shaping the understanding of the causes of obesity. © 2014 American Cancer Society.


Tu H.,University of Illinois at Urbana - Champaign
Nature Photonics | Year: 2016

The preparation, staining, visualization and interpretation of histological images of tissue is well accepted as the gold standard process for the diagnosis of disease. These methods have a long history of development, and are used ubiquitously in pathology, despite being highly time- and labour-intensive. Here, we introduce a unique optical imaging platform and methodology for label-free multimodal multiphoton microscopy that uses a novel photonic-crystal fibre source to generate tailored chemical contrast based on programmable supercontinuum pulses. We demonstrate the collection of optical signatures of the tumour microenvironment, including evidence of mesoscopic biological organization, tumour cell migration and (lymph-) angiogenesis collected directly from fresh ex vivo mammary tissue. Acquisition of these optical signatures and other cellular or extracellular features, which are largely absent from histologically processed and stained tissue, combined with an adaptable platform for optical alignment-free programmable-contrast imaging, offers the potential to translate stain-free molecular histopathology into routine clinical use. © 2016 Nature Publishing Group


Wong G.C.L.,University of Illinois at Urbana - Champaign | Pollack L.,Cornell University
Annual Review of Physical Chemistry | Year: 2010

Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states. Copyright © 2010 by Annual Reviews. All rights reserved.


Cimpian A.,University of Illinois at Urbana - Champaign | Erickson L.C.,Carnegie Mellon University
Cognitive Psychology | Year: 2012

What are the representations and learning mechanisms that underlie conceptual development? The present research provides evidence in favor of the claim that this process is guided by an early-emerging predisposition to think and learn about abstract kinds. Specifically, three studies (N=192) demonstrated that 4- to 7-year-old children have better recall for novel information about kinds (e.g., that dogs catch a bug called " fep" ) than for similar information about individuals (e.g., that a particular dog catches a bug called " fep" ). By showing that children are particularly likely to retain information about kinds, this work not only provides a first empirical demonstration of a phenomenon that may be key to conceptual development but also makes it apparent that young children's thinking is suffused with abstractions rather than being perceptually-based and concrete. © 2011 Elsevier Inc.


Andrade F.C.,University of Illinois at Urbana - Champaign
The journals of gerontology. Series B, Psychological sciences and social sciences | Year: 2010

OBJECTIVES. The aim of the present study is to investigate differences in total life expectancy (TLE), disability-free life expectancy (DFLE), disabled life expectancy (DLE), and personal care assistance between individuals with and without diabetes in Mexico. METHODS: The sample was drawn from the nationally representative Mexican Health and Aging Study. Disability was assessed through a basic Activities of Daily Living (ADL) measure, the Instrumental Activities of Daily Living (IADL) scale, and the Nagi physical performance measure. The Interpolation of Markov Chains method was used to estimate the impact of diabetes on TLE and DFLE. RESULTS: Results indicate that diabetes reduces TLE at ages 50 and 80 by about 10 and 4 years, respectively. Diabetes is also associated with fewer years in good health. DFLE (based on ADL measures) at age 50 is 20.8 years (95% confidence interval [CI]: 19.2-22.3) for those with diabetes, compared with 29.9 years (95% CI: 28.8-30.9) for those without diabetes. Regardless of diabetes status, Mexican women live longer but face a higher disability burden than men. CONCLUSION: Among older adults in Mexico, diabetes is associated with shorter TLE and DFLE. The negative effect of diabetes on the number of years lived, particularly in good health, creates significant economic, social, and individual costs for elderly Mexicans.


Oldfield E.,University of Illinois at Urbana - Champaign
Accounts of Chemical Research | Year: 2010

The isoprenoid biosynthesis pathways produce the largest class of small molecules in Nature: isoprenoids (also called terpenoids). Not surprisingly then, isoprenoid biosynthesis is a target for drug discovery, and many drugs-such as Lipitor (used to lower cholesterol), Fosamax (used to treat osteoporosis), and many anti-infectives-target isoprenoid biosynthesis. However, drug resistance in malaria, tuberculosis, and staph infections is rising, cheap and effective drugs for the neglected tropical diseases are lacking, and progress in the development of anticancer drugs is relatively slow. Isoprenoid biosynthesis is thus an attractive target, and in this Account, I describe developments in four areas, using in each case knowledge derived from one area of chemistry to guide the development of inhibitors (or drug leads) in another, seemingly unrelated, area. First, I describe mechanistic studies of the enzyme IspH, which is present in malaria parasites and most pathogenic bacteria, but not in humans. IspH is a 4Fe-4S protein and produces the five-carbon (C5) isoprenoids IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphate) from HMBPP (E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate) via a 2H +/2e- reduction (of an allyl alcohol to an alkene). The mechanism is unusual in that it involves organometallic species: "metallacycles" (n2-alkenes) and n1/n 3-allyls. These observations lead to novel alkyne inhibitors, which also form metallacycles. Second, I describe structure-function-inhibition studies of FPP synthase, the macromolecule that condenses IPP and DMAPP to the sesquiterpene farnesyl diphosphate (FPP) in a "head-to-tail" manner. This enzyme uses a carbocation mechanism and is potently inhibited by bone resorption drugs (bisphosphonates), which I show are also antiparasitic agents that block sterol biosynthesis in protozoa. Moreover, "lipophilic" bisphosphonates inhibit protein prenylation and invasiveness in tumor cells, in addition to activating γΔ T-cells to kill tumor cells, and are important new leads in oncology. Third, I describe structural and inhibition studies of a "head-to-head" triterpene synthase, dehydrosqualene synthase (CrtM), from Staphylococcus aureus. CrtM catalyzes the first committed step in biosynthesis of the carotenoid virulence factor staphyloxanthin: the condensation of two FPP molecules to produce a cyclopropane (presqualene diphosphate). The structure of CrtM is similar to that of human squalene synthase (SQS), and some SQS inhibitors (originally developed as cholesterol-lowering drugs) block staphyloxanthin biosynthesis. Treated bacteria are white and nonvirulent (because they lack the carotenoid shield that protects them from reactive oxygen species produced by neutrophils), rendering them susceptible to innate immune system clearance-a new therapeutic approach. And finally, I show that the heart drug amiodarone, also known to have antifungal activity, blocks ergosterol biosynthesis at the level of oxidosqualene cyclase in Trypanosoma cruzi, work that has led to its use in the clinic as a novel antiparasitic agent. In each of these four examples, I use information from one area (organometallic chemistry, bone resorption drugs, cholesterol-lowering agents, heart disease) to develop drug leads in an unrelated area: a "knowledge-based" approach that represents an important advance in the search for new drugs. © 2010 American Chemical Society.


Comellas G.,Center for Biophysics and Computational Biology | Rienstra C.M.,Center for Biophysics and Computational Biology | Rienstra C.M.,University of Illinois at Urbana - Champaign
Annual Review of Biophysics | Year: 2013

Protein structure determination methods using magic-angle spinning solid-state nuclear magnetic resonance (MAS SSNMR) have experienced a remarkable development in the past decade. Significant advances in instrumentation, sample preparation, spectroscopic techniques, and computational methods have made possible the determination of the first high-resolution structures of a peptide and a protein in 2002. Subsequent developments allowed the investigation of larger proteins, the initial application of automated analysis routines, and substantial improvements in structural resolution. The application of these methods has enabled the investigation of amyloid fibril structures, conformational dynamics, and their assembly pathways at an atomic level for the first time, as these are systems not accessible by other common techniques. Recent advances and future trends for protein structure determination using MAS SSNMR, as well as its application to the study of amyloid fibrils, are reviewed. Copyright © 2013 by Annual Reviews.


Ha T.,Center for the Physics of Living Cells | Ha T.,University of Illinois at Urbana - Champaign | Kozlov A.G.,University of Washington | Lohman T.M.,University of Washington
Annual Review of Biophysics | Year: 2012

The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical, and magnetic tweezers), in combination with ensemble methods, have been particularly useful for mechanistic studies of proteinnucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single-molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single-stranded DNA. These include single-stranded DNA binding proteins, recombinases (RecARad51), and helicasestranslocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the single-stranded DNA and the mechanistic and functional information that can result from detailed analysis of such movement. © 2012 by Annual Reviews. All rights reserved.


Silverman S.K.,University of Illinois at Urbana - Champaign
Angewandte Chemie - International Edition | Year: 2010

Beyond biological DNA : Chemists are exploiting DNA for interesting applications as a catalyst, encoding component, and stereocontrol element. Each of these chemical applications takes advantage of a distinct subset of DNA's properties in ways not known in nature. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.


Stocum D.L.,Indiana University - Purdue University Indianapolis | Cameron J.A.,University of Illinois at Urbana - Champaign
Developmental Dynamics | Year: 2011

The experimental study of amphibian limb regeneration spans most of the 20th century and the first decade of the 21st century. We first review the major questions investigated over this time span: (1) the origin of regeneration blastema cells, the mechanism of tissue breakdown that liberates cells from their tissue organization to participate in blastema formation, (3) the mechanism of dedifferentiation of these cells, (4) how the blastema grows, (5) how the blastema is patterned to restore the missing limb structures, and (6) why adult anurans, birds and mammals do not have the regenerative powers of urodele salamanders. We then look forward in a perspective to discuss the many unanswered questions raised by investigations of the past century, what new approaches can be taken to answer them, and what the prospects are for translation of basic research on limb regeneration into clinical means to regenerate human appendages. © 2011 Wiley-Liss, Inc.


Sun N.,University of Illinois at Urbana - Champaign
Biotechnology and bioengineering | Year: 2013

Transcription activator-like effector (TALE) nucleases (TALENs) have recently emerged as a revolutionary genome editing tool in many different organisms and cell types. The site-specific chromosomal double-strand breaks introduced by TALENs significantly increase the efficiency of genomic modification. The modular nature of the TALE central repeat domains enables researchers to tailor DNA recognition specificity with ease and target essentially any desired DNA sequence. Here, we comprehensively review the development of TALEN technology in terms of scaffold optimization, DNA recognition, and repeat array assembly. In addition, we provide some perspectives on the future development of this technology. Copyright © 2013 Wiley Periodicals, Inc.


Forsyth D.A.,University of Illinois at Urbana - Champaign
International Journal of Computer Vision | Year: 2011

The shading on curved surfaces is a cue to shape. Current computer vision methods for analyzing shading use physically unrealistic models, have serious mathematical problems, cannot exploit geometric information if it is available, and are not reliable in practice. We introduce a novel method of accounting for variations in irradiance resulting from interreflections, complex sources and the like. Our approach uses a spatially varying source model with a local shading model. Fast spatial variation in the source is penalised, consistent with the rendering community's insight that interreflections are spatially slow. This yields a physically plausible shading model. Because modern cameras can make accurate reports of observed radiance, our method compels the reconstructed surface to have shading exactly consistent with that of the image. For inference, we use a variational formulation, with a selection of regularization terms which guarantee that a solution exists. Our method is evaluated on physically accurate renderings of virtual objects, and on images of real scenes, for a variety of different kinds of boundary condition. Reconstructions for single sources compare well with photometric stereo reconstructions and with ground truth. © 2010 Springer Science+Business Media, LLC.


Kamalabadi F.,University of Illinois at Urbana - Champaign
IEEE Signal Processing Magazine | Year: 2010

A unified approach based on the assumption of additive Gaussian noise and regularization theory that illustrates the flavor of multidimensional image reconstruction problems and the associated challenges, is presented. In such image formation scenarios involving multiple sensors or perspectives, the relationship between the set of observations and the unknown field can often be adequately characterized by a linear observation model. The response function is typically determined from the characteristics of the electromagnetic radiation propagating between the source and the detector. A common challenge in practical astronomical inverse imaging problems is that the resulting linear systems are typically of enormous dimension, requiring special considerations for obtaining feasible solutions. Variational and statistical formulation of the associated inverse problems address the incomplete data aspect of the problem, while a statespace formulation offers spatial-temporal estimation of nonstationary images.


Erickson J.,University of Illinois at Urbana - Champaign
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2010

We observe that the classical maximum flow problem in any directed planar graph G can be reformulated as a parametric shortest path problem in the oriented dual graph G*. This reformulation immediately suggests an algorithm to compute maximum flows, which runs in O(n log n) time. As we continuously increase the parameter, each change in the shortest path tree can be effected in O(log n) time using standard dynamic tree data structures, and the special structure of the parametrization implies that each directed edge enters the evolving shortest path tree at most once. The resulting maximum-flow algorithm is identical to the recent algorithm of Borradaile and Klein [J. ACM 2009], but our new formulation allows a simpler presentation and analysis. On the other hand, we demonstrate that for a similarly structured parametric shortest path problem on the torus, the shortest path tree can change Ω(n2) times in the worst case, suggesting that a different method may be required to efficiently compute maximum flows in higher-genus graphs. Copyright © by SIAM.


Zhang T.,Advanced Digital science Center | Ghanem B.,King Abdullah University of Science and Technology | Liu S.,National University of Singapore | Ahuja N.,University of Illinois at Urbana - Champaign
International Journal of Computer Vision | Year: 2013

In this paper, we formulate object tracking in a particle filter framework as a structured multi-task sparse learning problem, which we denote as Structured Multi-Task Tracking (S-MTT). Since we model particles as linear combinations of dictionary templates that are updated dynamically, learning the representation of each particle is considered a single task in Multi-Task Tracking (MTT). By employing popular sparsity-inducing lp,q mixed norms (specifically p∈2,∞ and q=1), we regularize the representation problem to enforce joint sparsity and learn the particle representations together. As compared to previous methods that handle particles independently, our results demonstrate that mining the interdependencies between particles improves tracking performance and overall computational complexity. Interestingly, we show that the popular L1 tracker (Mei and Ling, IEEE Trans Pattern Anal Mach Intel 33(11):2259-2272, 2011) is a special case of our MTT formulation (denoted as the L11 tracker) when p=q=1. Under the MTT framework, some of the tasks (particle representations) are often more closely related and more likely to share common relevant covariates than other tasks. Therefore, we extend the MTT framework to take into account pairwise structural correlations between particles (e.g. spatial smoothness of representation) and denote the novel framework as S-MTT. The problem of learning the regularized sparse representation in MTT and S-MTT can be solved efficiently using an Accelerated Proximal Gradient (APG) method that yields a sequence of closed form updates. As such, S-MTT and MTT are computationally attractive. We test our proposed approach on challenging sequences involving heavy occlusion, drastic illumination changes, and large pose variations. Experimental results show that S-MTT is much better than MTT, and both methods consistently outperform state-of-the-art trackers. © 2012 Springer Science+Business Media New York.


Rauchfuss T.B.,University of Illinois at Urbana - Champaign
Angewandte Chemie - International Edition | Year: 2010

Take two cyanides and report to work! Cyanide is an essential ingredient of the [FeFe]-hydrogenases. Recent studies have revealed how nature makes these cyanide ligands coordinated to the diiron core of the active site (see structure). Rapidly unfolding research on the maturation process is revealing new dimensions of biosynthesis. The transformations discovered may lead to the development of useful organometallic reactions. (Figure Presented) © 2010 Wiley.VCH Verlag GrnbH & Co. KGaA, Weinheim biosynthesis, cofactors cyanide, hydrogenases, iron.


Dragic P.D.,University of Illinois at Urbana - Champaign
Journal of Lightwave Technology | Year: 2011

We present both modeling results and experimental data demonstrating that B2O3 (boric oxide) can be used as an effective SBS-suppressive optical fiber codopant due to a very large acoustic damping coefficient. A Ge-containing fiber with ∼6 wt% B2O3 at room temperature has a Brillouin gain coefficient more than 4 dB lower than that of standard Ge-doped SMF. These B-doped fibers, unlike standard Ge-doped SMF, have Brillouin spectra that broaden with increasing fiber temperature. Modeling parameters (acoustic velocity, spectral width, etc.) for bulk B 2O3 based on a fit-to-data are provided. Modeling results for the B-Ge-Si oxide system indicate that the bulk material gain falls below 0.5 × 10-11 m/W at 1534 nm near the 1B2O 3:4SiO 2 molar composition. © 2011 IEEE.


Tita G.E.,University of California at Irvine | Radil S.M.,University of Illinois at Urbana - Champaign
Journal of Quantitative Criminology | Year: 2011

The majority of spatial studies of crime employ an inductive approach in both the modeling and interpretation of the mechanisms of influence thought to be responsible for the patterning of crime in space and time. In such studies, the spatial weights matrix is specified without regard to the theorized mechanisms of influence between the units of analysis. Recently, a more deductive approach has begun to gain traction in which the theory of influence is used to model influence in geographic space. Using data from Los Angeles, we model the spatial distribution of gang violence by considering both the relative location of the gangs in space while simultaneously capturing their position within an enmity network of gang rivalries. We find that the spatial distribution of gang violence is more strongly associated with the socio-spatial dimensions of gang rivalries than it is with adjacency-based measures of spatial autocorrelation. © 2011 Springer Science+Business Media, LLC.


Tappenden K.A.,University of Illinois at Urbana - Champaign
JPEN. Journal of parenteral and enteral nutrition | Year: 2014

The human small intestine is organized with a proximal-to-distal gradient of mucosal structure and nutrient processing capacity. However, certain nutrients undergo site-specific digestion and absorption, such as iron and folate in the duodenum/jejunum vs vitamin B12 and bile salts in the ileum. Intestinal resection can result in short bowel syndrome (SBS) due to reduction of total and/or site-specific nutrient processing areas. Depending on the segment(s) of intestine resected, malabsorption can be nutrient specific (eg, vitamin B12 or fat) or sweeping, with deficiencies in energy, protein, and various micronutrients. Jejunal resections are generally better tolerated than ileal resections because of greater postresection adaptive capacity than that of the jejunum. Following intestinal resection, energy scavenging and fluid absorption become particularly important in the colon owing to loss of digestive and absorptive surface area in the resection portion. Resection-induced alterations in enteroendocrine cell abundance can further disrupt intestinal function. For example, patients with end jejunostomy have depressed circulating peptide YY and glucagon-like peptide 2 concentrations, which likely contribute to the rapid intestinal transit and blunted intestinal adaptation observed in this population. SBS-associated pathophysiology often extends beyond the gastrointestinal tract, with hepatobiliary disease, metabolic bone disease, D-lactic acidosis, and kidney stone formation being chronic complications. Clinical management of SBS must be individualized to account for the specific nutrient processing deficit within the remnant bowel and to mitigate potential complications, both inside and outside the gastrointestinal tract.


Liberzon D.,University of Illinois at Urbana - Champaign
Automatica | Year: 2014

We study the problem of asymptotically stabilizing a switched linear control system using sampled and quantized measurements of its state. The switching is assumed to be slow enough in the sense of combined dwell time and average dwell time, each individual mode is assumed to be stabilizable, and the available data rate is assumed to be large enough but finite. Our encoding and control strategy is rooted in the one proposed in our earlier work on non-switched systems, and in particular the data-rate bound used here is the data-rate bound from that earlier work maximized over the individual modes. The main technical step that enables the extension to switched systems concerns propagating over-approximations of reachable sets through sampling intervals, during which the switching signal is not known; a novel algorithm is developed for this purpose. Our primary focus is on systems with time-dependent switching (switched systems) but the setting of state-dependent switching (hybrid systems) is also discussed. © 2013 Elsevier Ltd. All rights reserved.


Leslie S.-J.,Princeton University | Cimpian A.,University of Illinois at Urbana - Champaign | Meyer M.,Otterbein University | Freeland E.,Princeton University
Science | Year: 2015

The gender imbalance in STEM subjects dominates current debates about women's underrepresentation in academia. However, women are well represented at the Ph.D. level in some sciences and poorly represented in some humanities (e.g., in 2011, 54% of U.S. Ph. D.'s in molecular biology were women versus only 31% in philosophy). We hypothesize that, across the academic spectrum, women are underrepresented in fields whose practitioners believe that raw, innate talent is the main requirement for success, because women are stereotyped as not possessing such talent. This hypothesis extends to African Americans' underrepresentation as well, as this group is subject to similar stereotypes. Results from a nationwide survey of academics support our hypothesis (termed the field-specific ability beliefs hypothesis) over three competing hypotheses. © 2015, American Association for the Advancement of Science. All rights reserved.


Roch S.,University of Wisconsin - Madison | Warnow T.,University of Illinois at Urbana - Champaign
Systematic Biology | Year: 2015

The estimation of species trees using multiple loci has become increasingly common. Because different loci can have different phylogenetic histories (reflected in different gene tree topologies) for multiple biological causes, new approaches to species tree estimation have been developed that take gene tree heterogeneity into account. Among these multiple causes, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is potentially the most common cause of gene tree heterogeneity, and much of the focus of the recent literature has been on how to estimate species trees in the presence of ILS. Despite progress in developing statistically consistent techniques for estimating species trees when gene trees can differ due to ILS, there is substantial controversy in the systematics community as to whether to use the new coalescent-based methods or the traditional concatenation methods. One of the key issues that has been raised is understanding the impact of gene tree estimation error on coalescent-based methods that operate by combining gene trees. Here we explore the mathematical guarantees of coalescent-based methods when analyzing estimated rather than true gene trees. Our results provide some insight into the differences between promise of coalescent-based methods in theory and their performance in practice. © 2015 The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.


Konigsberg L.W.,University of Illinois at Urbana - Champaign
American journal of physical anthropology | Year: 2013

In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available. Copyright © 2013 Wiley Periodicals, Inc.


Raginsky M.,University of Illinois at Urbana - Champaign | Sason I.,Technion - Israel Institute of Technology
Foundations and Trends in Communications and Information Theory | Year: 2013

During the last two decades, concentration inequalities have been the subject of exciting developments in various areas, including convex geometry, functional analysis, statistical physics, high-dimensional statistics, pure and applied probability theory (e.g., concentration of measure phenomena in random graphs, random matrices, and percolation), information theory, theoretical computer science, and learning theory. This monograph focuses on some of the key modern mathematical tools that are used for the derivation of concentration inequalities, on their links to information theory, and on their various applications to communications and coding. In addition to being a survey, this monograph also includes various new recent results derived by the authors. The first part of the monograph introduces classical concentration inequalities for martingales, as well as some recent refinements and extensions. The power and versatility of the martingale approach is exemplified in the context of codes defined on graphs and iterative decoding algorithms, as well as codes for wireless communication. The second part of the monograph introduces the entropy method, an information-theoretic technique for deriving concentration inequalities. The basic ingredients of the entropy method are discussed first in the context of logarithmic Sobolev inequalities, which underlie the so-called functional approach to concentration of measure, and then from a complementary information-theoretic viewpoint based on transportation-cost inequalities and probability in metric spaces. Some representative results on concentration for dependent random variables are briefly summarized, with emphasis on their connections to the entropy method. Finally, we discuss several applications of the entropy method to problems in communications and coding, including strong converses, empirical distributions of good channel codes, and an information-theoretic converse for concentration of measure. © 2013 M. Raginsky and I. Sason.


Saijo K.,University of California at San Diego | Collier J.G.,University of California at San Diego | Li A.C.,University of California at San Diego | Katzenellenbogen J.A.,University of Illinois at Urbana - Champaign | Glass C.K.,University of California at San Diego
Cell | Year: 2011

Microglia and astrocytes play essential roles in the maintenance of homeostasis within the central nervous system, but mechanisms that control the magnitude and duration of responses to infection and injury remain poorly understood. Here, we provide evidence that 5-androsten-3β,17β-diol (ADIOL) functions as a selective modulator of estrogen receptor (ER)β to suppress inflammatory responses of microglia and astrocytes. ADIOL and a subset of synthetic ERβ-specific ligands, but not 17β-estradiol, mediate recruitment of CtBP corepressor complexes to AP-1-dependent promoters, thereby repressing genes that amplify inflammatory responses and activate Th17 T cells. Reduction of ADIOL or ERβ expression results in exaggerated inflammatory responses to TLR4 agonists. Conversely, the administration of ADIOL or synthetic ERβ-specific ligands that promote CtBP recruitment prevents experimental autoimmune encephalomyelitis in an ERβ-dependent manner. These findings provide evidence for an ADIOL/ERβ/CtBP-transrepression pathway that regulates inflammatory responses in microglia and can be targeted by selective ERβ modulators. PaperClip: © 2011 Elsevier Inc.


Ostoja-Starzewski M.,University of Illinois at Urbana - Champaign
Zeitschrift fur Angewandte Mathematik und Physik | Year: 2013

Basic equations of electromagnetic fields in anisotropic fractal media are obtained using a dimensional regularization approach. First, a formulation based on product measures is shown to satisfy the four basic identities of the vector calculus. This allows a generalization of the Green-Gauss and Stokes theorems as well as the charge conservation equation on anisotropic fractals. Then, pursuing the conceptual approach, we derive the Faraday and Ampère laws for such fractal media, which, along with two auxiliary null-divergence conditions, effectively give the modified Maxwell equations. Proceeding on a separate track, we employ a variational principle for electromagnetic fields, appropriately adapted to fractal media, so as to independently derive the same forms of these two laws. It is next found that the parabolic (for a conducting medium) and the hyperbolic (for a dielectric medium) equations involve modified gradient operators, while the Poynting vector has the same form as in the non-fractal case. Finally, Maxwell's electromagnetic stress tensor is reformulated for fractal systems. In all the cases, the derived equations for fractal media depend explicitly on fractal dimensions in three different directions and reduce to conventional forms for continuous media with Euclidean geometries upon setting these each of dimensions equal to unity. © 2012 Springer Basel AG.


Dewalt R.E.,University of Illinois at Urbana - Champaign
Journal of the North American Benthological Society | Year: 2011

A taxonomic perspective of deoxyribonucleic acid (DNA) barcoding is presented here with respect to its use within the freshwater science community. The goals and methods of DNA barcoding and the criticisms leveled at the procedure by the taxonomic community are explained. The major goal of DNA-barcoding efforts is to aid identification of specimens by matching sequences to a sequence library. This goal is achievable, but barcoding efforts must be coupled with a much wider sampling regime and should be done with the full cooperation and collaboration of the taxonomic community. Through collaborative efforts, taxonomists and barcode advocates can build capacity for taxonomy and sequence the vast number of specimens needed to build a truly comprehensive barcode library for use by benthic scientists. Other barcoding goals, such as species diagnosis and biodiversity surveys, are more problematic, but solutions are possible. © 2011 The North American Benthological Society.


Kadloor S.,University of Illinois at Urbana - Champaign | Adve R.,Kings College
IEEE Transactions on Wireless Communications | Year: 2010

We consider a system with a single base station communicating with multiple users over orthogonal channels while being assisted by multiple relays. Several recent works have suggested that, in such a scenario, selection, i.e., a single relay helping the source, is the best relaying option in terms of the resulting complexity and overhead. However, in a multiuser setting, optimal relay assignment is a combinatorial problem. In this paper, we formulate a related convex optimization problem that provides an extremely tight upper bound on performance and show that selection is, almost always, inherent in the solution. We also provide a heuristic to find a close-to-optimal relay assignment and power allocation across users supported by a single relay. Simulation results using realistic channel models demonstrate the efficacy of the proposed schemes, but also raise the question as to whether the gains from relaying are worth the additional costs. © 2006 IEEE.


Kwon Y.,Konkuk University | Ceperley D.M.,University of Illinois at Urbana - Champaign
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We have performed path-integral Monte Carlo calculations to study 4He adsorption on a single graphene sheet. The 4He-substrate interaction was assumed to be a pairwise sum of the helium-carbon potentials constructed by Carlos and Cole to fit helium scattering data from a graphite surface. We employed both an anisotropic 6-12 Lennard-Jones potential and a spherical 6-12 potential. For both potentials, the first 4He layer has the C 1/3 commensurate structure at a surface density of 0.0636 -2. Vacancy states created in the C 1/3 commensurate solid, however, behave differently depending on the 4He-substrate interaction: a cluster of localized vacancies are formed with the fully anisotropic 6-12 pair potentials while mobile vacancies are found to induce finite superfluid fractions with the substrate potential based on only the isotropic parts of the inter-atomic pair potentials. For the second helium layer we find that exchange among 4He adatoms results in quantum melting of a C 7/12 commensurate structure, which is registered to a first-layer triangular solid. The possible stabilization of this commensurate structure with the addition of 3He impurities is discussed. © 2012 American Physical Society.


Cimpian A.,University of Illinois at Urbana - Champaign | Markman E.M.,Stanford University
Child Development | Year: 2011

These studies investigate how the distinction between generic sentences (e.g., "Boys are good at math") and nongeneric sentences (e.g., "Johnny is good at math") shapes children's social cognition. These sentence types are hypothesized to have different implications about the source and nature of the properties conveyed. Specifically, generics may be more likely to imply that the referred-to properties emerge naturally from an internal source, which may cause these properties to become essentialized. Four experiments (N=269 four-year-olds and undergraduates) confirmed this hypothesis but also suggested that participants only essentialize the information provided in generic form when this construal is consistent with their prior theoretical knowledge. These studies further current understanding of language as a means of learning about others. © 2011 The Authors. Child Development © 2011 Society for Research in Child Development, Inc..


Behzad B.,University of Illinois at Urbana - Champaign
Expert review of vaccines | Year: 2012

This paper analyzes pricing strategies for US pediatric combination vaccines by comparing the lowest overall cost formularies (i.e., formularies that have the lowest overall cost). Three pharmaceutical companies compete pairwise over the sale of monovalent and combination vaccines. Particular emphasis is placed on examining the price of Sanofi Pasteur's DTaP-IPV/HIb under different conditions. The main contribution of the paper is to provide the lowest overall cost formularies for different prices of DTaP-IPV/HIb and other Sanofi Pasteur vaccines. The resulting analysis shows that DTaP-IPV/HIb could have been more competitively priced compared with the combination vaccine DTaP-HepB-IPV, for federal contract prices in 2009, 2010 and 2011. This study also proposes the lowest overall cost formularies when shortages of monovalent vaccines occur.


Hurley W.L.,University of Illinois at Urbana - Champaign
Nutrients | Year: 2011

Immunoglobulins form an important component of the immunological activity found in milk and colostrum. They are central to the immunological link that occurs when the mother transfers passive immunity to the offspring. The mechanism of transfer varies among mammalian species. Cattle provide a readily available immune rich colostrum and milk in large quantities, making those secretions important potential sources of immune products that may benefit humans. Immune milk is a term used to describe a range of products of the bovine mammary gland that have been tested against several human diseases. The use of colostrum or milk as a source of immunoglobulins, whether intended for the neonate of the species producing the secretion or for a different species, can be viewed in the context of the types of immunoglobulins in the secretion, the mechanisms by which the immunoglobulins are secreted, and the mechanisms by which the neonate or adult consuming the milk then gains immunological benefit. The stability of immunoglobulins as they undergo processing in the milk, or undergo digestion in the intestine, is an additional consideration for evaluating the value of milk immunoglobulins. This review summarizes the fundamental knowledge of immunoglobulins found in colostrum, milk, and immune milk.


Sage W.M.,University of Texas at Austin | Hyman D.A.,University of Illinois at Urbana - Champaign
Health Affairs | Year: 2014

Physician leadership is required to improve the efficiency and reliability of the US health care system, but many physicians remain lukewarm about the changes needed to attain these goals. Malpractice liability-a sore spot for decades-may exacerbate physician resistance. The politics of malpractice have become so lawyer-centric that recognizing the availability of broader gains from trade in tort reform is an important insight for health policy makers. To obtain relief from malpractice liability, physicians may be willing to accept other policy changes that more directly improve access to care and reduce costs. For example, the American Medical Association might broker an agreement between health reform proponents and physicians to enact federal legislation that limits malpractice liability and simultaneously restructures fee-for-service payment, heightens transparency regarding the quality and cost of health care services, and expands practice privileges for other health professionals. There are also reasons to believe that tort reform can make ongoing health care delivery reforms work better, in addition to buttressing health reform efforts that might otherwise fail politically. © 2014 Project HOPE- The People-to-People Health Foundation, Inc.


Cheng J.,University of Illinois at Urbana - Champaign | Deming T.J.,University of California at Los Angeles
Topics in Current Chemistry | Year: 2012

This chapter summarizes methods for the synthesis of polypeptides by ring-opening polymerization. Traditional and recently improved methods used to polymerize α-amino acid N-carboxyanhydrides (NCAs) for the synthesis of homopolypeptides are described. Use of these methods and strategies for the preparation of block copolypeptides and side-chain-functionalized polypeptides are also presented, as well as an analysis of the synthetic scope of different approaches. Finally, issues relating to obtaining highly functional polypeptides in pure form are detailed. © 2011 Springer-Verlag Berlin Heidelberg.


Neubauer M.S.,University of Illinois at Urbana - Champaign
Annual Review of Nuclear and Particle Science | Year: 2011

This article is devoted to the physics of pairs of electroweak gauge bosons (dibosons) produced at high-energy particle colliders. Particular emphasis is placed on published results on diboson production from the CDF and DØ experiments at the Fermilab Tevatron and the CMS and ATLAS experiments at the CERN Large Hadron Collider (LHC). The study of diboson production at colliders plays an important role in tests of electroweak theory and searches for new phenomena at the TeV-energy scale and beyond. The diboson physics program has been a highlight of Run II at the Fermilab Tevatron. The progress made on analysis methods through the study of Standard Model diboson signals has had a direct and positive impact on the sensitivity of Higgs boson and New Physics searches in the Tevatron experiments. It is anticipated that diboson physics will play an even bigger role in the TeV-scale exploration now under way at the LHC. © 2011 by Annual Reviews. All rights reserved.


Dahmen K.A.,University of Illinois at Urbana - Champaign | Ben-Zion Y.,University of Southern California | Uhl J.T.,450 Las Lomas
Nature Physics | Year: 2011

Slowly sheared granular materials at high packing fractions deform via slip avalanches with a broad range of sizes. Conventional continuum descriptions are not expected to apply to such highly inhomogeneous, intermittent deformations. Here, we show that it is possible to analytically compute the dynamics using a simple model that is inherently discrete. This model predicts quantities such as the avalanche size distribution, power spectra and temporal avalanche profiles as functions of the grain number fraction v and the frictional weakening ε. A dynamical phase diagram emerges with quasi-static avalanches at high number fractions, and more regular, fluid-like flow at lower number fractions. The predictions agree with experiments and simulations for different granular materials, motivate future experiments and provide a fresh approach to data analysis. The simplicity of the model reveals quantitative connections to plasticity and earthquake statistics. © 2011 Macmillan Publishers Limited. All rights reserved.


Nedic A.,University of Illinois at Urbana - Champaign | Ozdaglar A.,Massachusetts Institute of Technology | Parrilo P.A.,Massachusetts Institute of Technology
IEEE Transactions on Automatic Control | Year: 2010

We present distributed algorithms that can be used by multiple agents to align their estimates with a particular value over a network with time-varying connectivity. Our framework is general in that this value can represent a consensus value among multiple agents or an optimal solution of an optimization problem, where the global objective function is a combination of local agent objective functions. Our main focus is on constrained problems where the estimates of each agent are restricted to lie in different convex sets. To highlight the effects of constraints, we first consider a constrained consensus problem and present a distributed "projected consensus algorithm" in which agents combine their local averaging operation with projection on their individual constraint sets. This algorithm can be viewed as a version of an alternating projection method with weights that are varying over time and across agents. We establish convergence and convergence rate results for the projected consensus algorithm.We next study a constrained optimization problem for optimizing the sum of local objective functions of the agents subject to the intersection of their local constraint sets. We present a distributed "projected subgradient algorithm" which involves each agent performing a local averaging operation, taking a subgradient step to minimize its own objective function, and projecting on its constraint set. We show that, with an appropriately selected stepsize rule, the agent estimates generated by this algorithm converge to the same optimal solution for the cases when the weights are constant and equal, and when the weights are time-varying but all agents have the same constraint set. © 2006 IEEE.


Davis B.J.,University of Illinois at Urbana - Champaign
Analytical chemistry | Year: 2010

Midinfrared (IR) microspectroscopy is widely employed for spatially localized spectral analyses. A comprehensive theoretical model for the technique, however, has not been previously proposed. In this paper, rigorous theory is presented for IR absorption microspectroscopy by using Maxwell's equations to model beam propagation. Focusing effects, material dispersion, and the geometry of the sample are accounted to predict spectral response for homogeneous samples. Predictions are validated experimentally using Fourier transform IR (FT-IR) microspectroscopic examination of a photoresist. The results emphasize that meaningful interpretation of IR microspectroscopic data must involve an understanding of the coupled optical effects associated with the sample, substrate properties, and microscopy configuration. Simulations provide guidance for developing experimental methods and future instrument design by quantifying distortions in the recorded data. Distortions are especially severe for transflection mode and for samples mounted on certain substrates. Last, the model generalizes to rigorously consider the effects of focusing. While spectral analyses range from examining gross spectral features to assessing subtle features using advanced chemometrics, the limitations imposed by these effects in the data acquisition on the information available are less clear. The distorting effects are shown to be larger than noise levels seen in modern spectrometers. Hence, the model provides a framework to quantify spectral distortions that may limit the accuracy of information or present confounding effects in microspectroscopy.


Chee B.W.,University of Illinois at Urbana - Champaign
AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium | Year: 2011

Adverse drug events (ADEs) remain a large problem in the United States, being the fourth leading cause of death, despite post market drug surveillance. Much post consumer drug surveillance relies on self-reported "spontaneous" patient data. Previous work has performed datamining over the FDA's Adverse Event Reporting System (AERS) and other spontaneous reporting systems to identify drug interactions and drugs correlated with high rates of serious adverse events. However, safety problems have resulted from the lack of post marketing surveillance information about drugs, with underreporting rates of up to 98% within such systems. We explore the use of online health forums as a source of data to identify drugs for further FDA scrutiny. In this work we aggregate individuals' opinions and review of drugs similar to crowd intelligence3. We use natural language processing to group drugs discussed in similar ways and are able to successfully identify drugs withdrawn from the market based on messages discussing them before their removal.


Vu L.,University of Washington | Liberzon D.,University of Illinois at Urbana - Champaign
IEEE Transactions on Automatic Control | Year: 2011

We consider the problem of adaptively stabilizing linear plants with unknown time-varying parameters in the presence of noise, disturbances, and unmodeled dynamics using the supervisory control framework, which employs multiple candidate controllers and an estimator based switching logic to select the active controller at every instant of time. Time-varying uncertain linear plants can be stabilized by supervisory control, provided that the plant's parameter varies slowly enough in terms of mixed dwell-time switching and average dwell-time switching, the noise and disturbances are bounded and small enough in terms of L-infinity norms, and the unmodeled dynamics are small enough in the input-to-state stability sense. This work extends previously reported works on supervisory control of linear time-invariant systems with constant unknown parameters to the case of linear time-varying uncertain systems. A numerical example is included, and limitations of the approach are discussed. © 2010 IEEE.


Subramanian R.,University of Illinois at Urbana - Champaign
Journal of vision | Year: 2014

A basic question in vision research regards where people look in complex scenes and how this influences their performance in various tasks. Previous studies with static images have demonstrated a close link between where people look and what they remember. Here, we examined the pattern of eye movements when participants watched neutral and emotional clips from Hollywood-style movies. Participants answered multiple-choice memory questions concerning visual and auditory scene details immediately upon viewing 1-min-long neutral or emotional movie clips. Fixations were more narrowly focused for emotional clips, and immediate memory for object details was worse compared to matched neutral scenes, implying preferential attention to emotional events. Although we found the expected correlation between where people looked and what they remembered for neutral clips, this relationship broke down for emotional clips. When participants were subsequently presented with key frames (static images) extracted from the movie clips such that presentation duration of the target objects (TOs) corresponding to the multiple-choice questions was matched and the earlier questions were repeated, more fixations were observed on the TOs, and memory performance also improved significantly, confirming that emotion modulates the relationship between gaze position and memory performance. Finally, in a long-term memory test, old/new recognition performance was significantly better for emotional scenes as compared to neutral scenes. Overall, these results are consistent with the hypothesis that emotional content draws eye fixations and strengthens memory for the scene gist while weakening encoding of peripheral scene details.


Fabiani M.,University of Illinois at Urbana - Champaign
Psychophysiology | Year: 2012

This paper reviews research on age-related changes in working memory and attention control. This work is interpreted within a framework labeled "GOLDEN aging" (growing of lifelong differences explains normal aging), which is based on the idea that normal aging (as opposed to pathological aging) represents maturational processes causing progressive shifts in the distributions of mental abilities over the lifespan. As such, brain phenomena observed in normal aging are already apparent, under appropriate conditions, in younger adults. Among the phenomena that can be interpreted according to the GOLDEN aging framework are reductions in working memory capacity, impairments of inhibitory processes, increases in frontal lobe activation, and lack of suppression of responses as a function of repetition. © 2012 Society for Psychophysiological Research.


Wang X.,University of Illinois at Urbana - Champaign | Lemmon M.,University of Notre Dame
Automatica | Year: 2011

This paper studies event design in event-triggered feedback systems. A novel event-triggering scheme is presented to ensure exponential stability of the resulting sampled-data system. The scheme postpones the triggering of events over previously proposed methods and therefore enlarges the intersampling period. The resulting intersampling periods and deadlines are bounded strictly away from zero when the continuous time system is input-to-state stable with respect to measurement errors. © 2011 Elsevier Ltd. All rights reserved.


Cahill D.G.,University of Illinois at Urbana - Champaign
MRS Bulletin | Year: 2012

Thermal conductivity is a familiar property of materials: silver conducts heat well, and plastic does not. In recent years, an interdisciplinary group of materials scientists, engineers, physicists, and chemists have succeeded in pushing back long-established limits in the thermal conductivity of materials. Carbon nanotubes and graphene are at the high end of the thermal conductivity spectrum due to their high sound velocities and relative lack of processes that scatter phonons. Unfortunately, the superlative thermal properties of carbon nanotubes have not found immediate application in composites or interface materials because of difficulties in making good thermal contact with the nanotubes. At the low end of the thermal conductivity spectrum, solids that combine order and disorder in the random stacking of two-dimensional crystalline sheets, so-called disordered layered crystals, show a thermal conductivity that is only a factor of 2 larger than air. The cause of this low thermal conductivity may be explained by the large anisotropy in elastic constants that suppresses the density of phonon modes that propagate along the soft direction. Low-dimensional quantum magnets demonstrate that electrons and phonons are not the only significant carriers of heat. Near room temperature, the spin thermal conductivity of spin-ladders is comparable to the electronic thermal conductivities of metals. Our measurements of nanoscale thermal transport properties employ a variety of ultrafast optical pump-probe metrology tools that we have developed over the past several years. We are currently working to extend these techniques to high pressures (60 GPa), high magnetic fields (5 T), and high temperatures (1000 K). © 2012 2012 Materials Research Society.


Pop E.,University of Illinois at Urbana - Champaign | Varshney V.,Air Force Research Lab | Roy A.K.,Air Force Research Lab
MRS Bulletin | Year: 2012

Graphene is a two-dimensional (2D) material with over 100-fold anisotropy of heat flow between the in-plane and out-of-plane directions. High in-plane thermal conductivity is due to covalent sp 2bonding between carbon atoms, whereas out-of-plane heat flow is limited by weak van der Waals coupling. Herein, we review the thermal properties of graphene, including its specific heat and thermal conductivity (from diffusive to ballistic limits) and the influence of substrates, defects, and other atomic modifications. We also highlight practical applications in which the thermal properties of graphene play a role. For instance, graphene transistors and interconnects benefit from the high in-plane thermal conductivity, up to a certain channel length. However, weak thermal coupling with substrates implies that interfaces and contacts remain significant dissipation bottlenecks. Heat flow in graphene or graphene composites could also be tunable through a variety of means, including phonon scattering by substrates, edges, or interfaces. Ultimately, the unusual thermal properties of graphene stem from its 2D nature, forming a rich playground for new discoveries of heat-flow physics and potentially leading to novel thermal management applications. © Copyright 2012 Materials Research Society.


McDonough J.P.,University of Illinois at Urbana - Champaign
Journal of the American Society for Information Science and Technology | Year: 2011

The Preserving Virtual Worlds project has been investigating the preservation of computer games and interactive fiction. The preservation of games benefits from simultaneous application of the data models from the Functional Requirements for Bibliographic Records report, and the Open Archival Information System reference model. The article described efforts to integrate these two data models within a single Web ontology language for application with multiple XML-based packaging formats. © 2010 ASIS&T.


Hammes-Schiffer S.,University of Illinois at Urbana - Champaign
Journal of the American Chemical Society | Year: 2015

Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa's for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future. © 2015 American Chemical Society.


Dig D.,University of Illinois at Urbana - Champaign
IEEE Software | Year: 2011

In the multicore era, a major programming task will be to make programs more parallel. This is tedious because it requires changing many lines of code; it's also error-prone and nontrivial because programmers need to ensure noninterference of parallel operations. Fortunately, interactive refactoring tools can help reduce the analysis and transformation burden. The author describes how refactoring tools can improve programmer productivity, program performance, and program portability. The article also describes a toolset that supports several refactorings for making programs thread-safe, threading sequential programs for throughput, and improving scalability of parallel programs.


Efron M.,University of Illinois at Urbana - Champaign
Journal of the American Society for Information Science and Technology | Year: 2011

Modern information retrieval (IR) has come to terms with numerous new media in efforts to help people find information in increasingly diverse settings. Among these new media are so-called microblogs. A microblog is a stream of text that is written by an author over time. It comprises many very brief updates that are presented to the microblog's readers in reverse-chronological order. Today, the service called Twitter is the most popular microblogging platform. Although microblogging is increasingly popular, methods for organizing and providing access to microblog data are still new. This review offers an introduction to the problems that face researchers and developers of IR systems in microblog settings. After an overview of microblogs and the behavior surrounding them, the review describes established problems in microblog retrieval, such as entity search and sentiment analysis, and modeling abstractions, such as authority and quality. The review also treats user-created metadata that often appear in microblogs. Because the problem of microblog search is so new, the review concludes with a discussion of particularly pressing research issues yet to be studied in the field. © 2011 ASIS&T.


Ferguson G.M.,University of Illinois at Urbana - Champaign
Child Development Perspectives | Year: 2013

New research with Jamaican adolescents has brought acculturation science into closer accord with two 21st-century cultural realities: (a) multicultural destination societies for immigrant families and (b) intercultural contact among nonimmigrant families via modern globalization mechanisms. In this article, I review two theoretical expansions to the traditional conceptualization of acculturation (i.e., tridimensional acculturation and remote acculturation) along with supporting empirical evidence among Jamaican adolescents in the United States and on the Caribbean island. First, bidimensional acculturation lenses are exchanged for tridimensional ones to capture the acculturation of immigrant youth for whom three cultural dimensions are relevant. Second, acculturation pathways are expanded to include modern indirect and/or intermittent intercultural contact for nonimmigrant youth. Tridimensional and remote acculturation may be modern mechanisms by which today's and tomorrow's adolescents produce their own development. These advances reveal new avenues to investigate adolescent acculturation and adaptation in their increasingly complex cultural neighborhoods. © 2013 The Society for Research in Child Development.


Kammel P.,University of Illinois at Urbana - Champaign | Kubodera K.,University of South Carolina
Annual Review of Nuclear and Particle Science | Year: 2010

A new generation of experiments is studying muon capture on hydrogen, deuterium, and 3He with significantly improved precision using a novel active-target method. At the same time, chiral effective field theories (EFTs) allow the calculation of low-energy electroweak observables on protons and the simplest nuclei within a rigorous quantum chromodynamics (QCD)-based framework. This experimental and theoretical progress significantly enhances our understanding of the axial current. In the case of the nucleon, the unambiguous experimental determination of the pseudoscalar coupling gP clarifies a long-standing puzzle and provides a basic test of QCD at low energies. In the case of deuterium and 3He, the new precision data allow a comprehensive test of EFT calculations of weak few-body reactions and determine an essential low-energy constant relevant for related astrophysics reactions of fundamental interest. © 2010 by Annual Reviews. All rights reserved.


Ren X.,University of Illinois at Urbana - Champaign | Lin Z.,Peking University
International Journal of Computer Vision | Year: 2013

Transform invariant low-rank textures (TILT) is a novel and powerful tool that can effectively rectify a rich class of low-rank textures in 3D scenes from 2D images despite significant deformation and corruption. The existing algorithm for solving TILT is based on the alternating direction method. It suffers from high computational cost and is not theoretically guaranteed to converge to a correct solution to the inner loop. In this paper, we propose a novel algorithm to speed up solving TILT, with guaranteed convergence for the inner loop. Our method is based on the recently proposed linearized alternating direction method with adaptive penalty. To further reduce computation, warm starts are also introduced to initialize the variables better and cut the cost on singular value decomposition. Extensive experimental results on both synthetic and real data demonstrate that this new algorithm works much more efficiently and robustly than the existing algorithm. It could be at least five times faster than the previous method. © 2013 Springer Science+Business Media New York.


Freund J.B.,University of Illinois at Urbana - Champaign
Annual Review of Fluid Mechanics | Year: 2014

The cellular detail of blood is an essential factor in its flow, especially in vessels or devices with size comparable to that of its suspended cells. This article motivates and reviews numerical simulation techniques that provide a realistic description of cell-scale blood flow by explicitly representing its coupled fluid and solid mechanics. Red blood cells are the principal focus because of their importance and because of their remarkable deformability, which presents particular simulation challenges. Such simulations must couple discretizations of the large-deformation elasticity of the cells with the viscous flow mechanics of the suspension. The Reynolds numbers are low, so the effectively linear fluid mechanics is amenable to a wide range of simulation methods, although the constitutive models and geometric factors of the coupled system introduce challenging nonlinearity. Particular emphasis is given to the relative merits of several fundamentally different simulation methods. The detailed description provided by such simulations is invaluable for advancing our scientific understanding of blood flow, and their ultimate impact will be in the design of biomedical tools and interventions. Copyright © 2014 by Annual Reviews. All rights reserved.


Ceperley D.M.,University of Illinois at Urbana - Champaign
Reviews in Mineralogy and Geochemistry | Year: 2010

In this brief article, various types of quantum Monte Carlo (QMC) methods are introduced, in particular, those that are applicable to systems in extreme regimes of temperature and pressure. References to longer articles have been given where detailed discussion of applications and algorithms appear. Copyright © Mineralogical Society of America.


Anastasio T.J.,University of Illinois at Urbana - Champaign
Frontiers in Pharmacology | Year: 2013

According to the amyloid hypothesis, Alzheimer Disease results from the accumulation beyond normative levels of the peptide amyloid-β (Aβ). Perhaps because of its pathological potential, Aβ and the enzymes that produce it are heavily regulated by the molecular interactions occurring within cells, including neurons. This regulation involves a highly complex system of intertwined normative and pathological processes, and the sex hormone estrogen contributes to it by influencing the Aβ-regulation system at many different points. Owing to its high complexity, Aβ regulation and the contribution of estrogen are very difficult to reason about. This report describes a computational model of the contribution of estrogen to Aβ regulation that provides new insights and generates experimentally testable and therapeutically relevant predictions. The computational model is written in the declarative programming language known as Maude, which allows not only simulation but also analysis of the system using temporal-logic. The model illustrates how the various effects of estrogen could work together to reduce Aβ levels, or prevent them from rising, in the presence of pathological triggers. The model predicts that estrogen itself should be more effective in reducing Aβ than agonists of estrogen receptor α (ERα), and that agonists of ERβ should be ineffective. The model shows how estrogen itself could dramatically reduce Aβ, and predicts that non-steroidal anti-inflammatory drugs should provide a small additional benefit. It also predicts that certain compounds, but not others, could augment the reduction in Aβ due to estrogen. The model is intended as a starting point for a computational/experimental interaction in which model predictions are tested experimentally, the results are used to confirm, correct, and expand the model, new predictions are generated, and the process continues, producing a model of ever increasing explanatory power and predictive value. © 2013 Anastasio.


Efron M.,University of Illinois at Urbana - Champaign
Journal of the American Society for Information Science and Technology | Year: 2010

Common measures of term importance in information retrieval (IR) rely on counts of term frequency; rare terms receive higher weight in document ranking than common terms receive. However, realistic scenarios yield additional information about terms in a collection. Of interest in this article is the temporal behavior of terms as a collection changes over time. We propose capturing each term's collection frequency at discrete time intervals over the lifespan of a corpus and analyzing the resulting time series. We hypothesize the collection frequency of a weakly discriminative term x at time t is predictable by a linear model of the term's prior observations. On the other hand, a linear time series model for a strong discriminators' collection frequency will yield a poor fit to the data. Operationalizing this hypothesis, we induce three time-based measures of term importance and test these against state-of-the-art term weighting models. © 2010 ASIS&T.


Zhu W.,University of Illinois at Urbana - Champaign
Research Quarterly for Exercise and Sport | Year: 2013

Setting standards and cutoff scores is essential to any measurement and evaluation practice. Two evaluation frameworks, norm-referenced (NR) and criterion-referenced (CR), have often been used for setting standards. Although setting fitness standards based on the NR evaluation is relatively easy as long as a nationally representative sample can be obtained and regularly updated, it has several limitations - namely, time dependency, population dependence, discouraging low-level performers, and favoring advantaged or punishing disadvantaged individuals. Fortunately, these limitations can be significantly eliminated by employing the CR evaluation, which was introduced to kinesiology by Safrit and colleagues in the 1980s and has been successfully applied to some practical problems (e.g., set health-related fitness standards for FITNESSGRAM®). Yet, the CR evaluation has its own challenges, e.g., selecting an appropriate measure for a criterion behavior, when the expected relationship between the criterion behavior and a predictive measure is not clear, and when standards are not consistent among multiple field measures. Some of these challenges can be addressed by employing the latest statistical methods (e.g., test equating). This article provides a comprehensive review of the science and art of setting standards and cutoff scores in kinesiology. After a brief historical overview of the standard-setting practice in kinesiology is presented, a case analysis of a successful CR evaluation, along with related challenges, is described. Lessons learned from past and current practice as well as how to develop a defendable standard are described. Finally, future research needs and directions are outlined. Copyright © AAHPERD.


Wang Z.,University of Illinois at Urbana - Champaign
Journal of the Atmospheric Sciences | Year: 2012

The thermodynamic aspects of tropical cyclone (TC) formation near the center of the wave pouch, a region of approximately closed Lagrangian circulation within the wave critical layer, are examined through diagnoses of a high-resolution numerical simulation and dropsonde data from a recent field campaign. It is found that the meso-b area near the pouch center is characterized by high saturation fraction, small difference in equivalent potential temperature Θ e between the surface and the middle troposphere, and a short incubation time scale. Updrafts tend to be more vigorous in this region, presumably because of reduced dry air entrainment, while downdrafts are not suppressed. The thermodynamic conditions near the pouch center are thus critically important for TC formation. The balanced responses to convective and stratiform heating at the pregenesis stage are examined using the Sawyer-Eliassen equation. Deep convection is concentrated near the pouch center. The strong radial and vertical gradients of latent heat release effectively force the transverse circulation and spin up a surface protovortex near the pouch center. Stratiform heating induces modest midlevel inflow and very weak lowlevel outflow, which contributes to the midlevel spinup without substantially spinning down the low-level circulation. The analysis of dropsonde data shows that the midlevel Θ e increases significantly near the pouch center one to two days prior to genesis but changes little away from the pouch center. This may indicate convective organization and the impending TC genesis. It also suggests that the critical information of TC genesis near the pouch center may be masked out if a spatial average is taken over the pouch scale. © 2012 American Meteorological Society.


Single-cell mass spectrometry (MS) empowers metabolomic investigations by decreasing analytical dimensions to the size of individual cells and subcellular structures. We describe a protocol for investigating and quantifying metabolites in individual isolated neurons using single-cell capillary electrophoresis (CE) coupled to electrospray ionization (ESI) time-of-flight (TOF) MS. The protocol requires ∼2 h for sample preparation, neuron isolation and metabolite extraction, and 1 h for metabolic measurement. We used the approach to detect more than 300 distinct compounds in the mass range of typical metabolites in various individual neurons (25-500 μm in diameter) isolated from the sea slug (Aplysia californica) central and rat (Rattus norvegicus) peripheral nervous systems. We found that a subset of identified compounds was sufficient to reveal metabolic differences among freshly isolated neurons of different types and changes in the metabolite profiles of cultured neurons. The protocol can be applied to the characterization of the metabolome in a variety of smaller cells and/or subcellular domains.


Chew H.B.,University of Illinois at Urbana - Champaign
Journal of the Mechanics and Physics of Solids | Year: 2013

Determining the tractions along a surface or interface from measurement data in the far-fields of nonlinear materials is a challenging inverse problem which has significant engineering and nanoscience applications. Previously, a field projection method was established to identify the crack-tip cohesive zone constitutive relations in an isotropic elastic solid (Hong and Kim, 2003. J. Mech. Phys. Solids 51, 1267). In this paper, the field projection method is further generalized to extracting the tractions along interfaces bounded by nonlinear materials, both with and without pre-existing cracks. The new formulation is based on Maxwell-Betti's reciprocal theorem with a reciprocity gap associated with nonlinear materials. We express the unknown normal and shear tractions along the interface in terms of the Fourier series, and use specially constructed analytical auxiliary fields in the reciprocal theorem to extract the unknown Fourier coefficients from far-field data; the reciprocity gap in the formulation is iteratively determined with a set of numerical algorithms. Our detailed numerical experiments demonstrate that this nonlinear field projection method (NFPM) is well-suited for extracting the interfacial tractions from the far-field data of any nonlinear elastic or elasto-plastic material with known constitutive laws. Applications of the NFPM to experiments and atomistic simulations are discussed. © 2012 Elsevier Ltd. All rights reserved.


Jia K.,University of Illinois at Urbana - Champaign | Wang X.,Chinese University of Hong Kong | Tang X.,Chinese University of Hong Kong
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2013

In this paper, we propose a framework of transforming images from a source image space to a target image space, based on learning coupled dictionaries from a training set of paired images. The framework can be used for applications such as image super-resolution and estimation of image intrinsic components (shading and albedo). It is based on a local parametric regression approach, using sparse feature representations over learned coupled dictionaries across the source and target image spaces. After coupled dictionary learning, sparse coefficient vectors of training image patch pairs are partitioned into easily retrievable local clusters. For any test image patch, we can fast index into its closest local cluster and perform a local parametric regression between the learned sparse feature spaces. The obtained sparse representation (together with the learned target space dictionary) provides multiple constraints for each pixel of the target image to be estimated. The final target image is reconstructed based on these constraints. The contributions of our proposed framework are three-fold. 1) We propose a concept of coupled dictionary learning based on coupled sparse coding which requires the sparse coefficient vectors of a pair of corresponding source and target image patches to have the same support, i.e., the same indices of nonzero elements. 2) We devise a space partitioning scheme to divide the high-dimensional but sparse feature space into local clusters. The partitioning facilitates extremely fast retrieval of closest local clusters for query patches. 3) Benefiting from sparse feature-based image transformation, our method is more robust to corrupted input data, and can be considered as a simultaneous image restoration and transformation process. Experiments on intrinsic image estimation and super-resolution demonstrate the effectiveness and efficiency of our proposed method. © 2012 IEEE.


Fu W.-T.,University of Illinois at Urbana - Champaign
Cognitive Science | Year: 2011

A dynamic context model of interactive behavior was developed to explain results from two experiments that tested the effects of interaction costs on encoding strategies, cognitive representations, and response selection processes in a decision-making and a judgment task. The model assumes that the dynamic context defined by the mixes of internal and external representations and processes are sensitive to the interaction cost imposed by the task environment. The model predicts that changes in the dynamic context may lead to systematic biases in cognitive representations and processes that eventually influence decision-making and judgment outcomes. Consistent with the predictions by the model, results from the experiments showed that as interaction costs increased, encoding strategies and cognitive representations shifted from perception-based to memory-based. Memory-based comparisons of the stimuli enhanced the similarity and dominance effects, and led to stronger systematic biases in response outcomes in a choice task. However, in a judgment task, memory-based representations enhanced only the dominance effects. Results suggested that systematic response biases in the dominance context were caused by biases in the cognitive representations of the stimuli, but response biases in the similarity context were caused by biases in the comparison process induced by the choice task. Results suggest that changes in interaction costs not only change whether information was assessed from the external world or from memory but also introduce systematic biases in the cognitive representation of the information, which act as biased inputs to the subsequent decision-making and judgment processes. Results are consistent with the idea of interactive cognition, which proposes that representations and processes are contingent on the dynamic context defined by the information flow between the external task environment and internal cognition. © 2011 Cognitive Science Society, Inc..


Fradkin E.,University of Illinois at Urbana - Champaign | Kivelson S.A.,Stanford University | Tranquada J.M.,Brookhaven National Laboratory
Reviews of Modern Physics | Year: 2015

The electronic phase diagrams of many highly correlated systems, and, in particular, the cuprate high temperature superconductors, are complex, with many different phases appearing with similar (sometimes identical) ordering temperatures even as material properties, such as dopant concentration, are varied over wide ranges. This complexity is sometimes referred to as "competing orders." However, since the relation is intimate, and can even lead to the existence of new phases of matter such as the putative "pair-density wave," the general relation is better thought of in terms of "intertwined orders." Some of the experiments in the cuprates which suggest that essential aspects of the physics are reflected in the intertwining of multiple orders, not just in the nature of each order by itself, are selectively analyzed. Several theoretical ideas concerning the origin and implications of this complexity are also summarized and critiqued. ©2015 American Physical Society.


Aksimentiev A.,University of Illinois at Urbana - Champaign
Nanoscale | Year: 2010

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics - a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores. © 2010 The Royal Society of Chemistry.


Valero M.C.,University of Illinois at Urbana - Champaign
Journal of Molecular Diagnostics | Year: 2011

Neurofibromatosis type 1 (NF1) is a hereditary disorder caused by mutations in the NF1 gene. Detecting mutation in NF1 is hindered by the gene's large size, the lack of mutation hotspots, the presence of pseudogenes, and the wide variety of possible lesions. We developed a method for detecting germline mutations by combining an original RNA-based cDNA-PCR mutation detection method and denaturing high-performance liquid chromatography (DHPLC) with multiplex ligation-dependent probe amplification (MLPA). The protocol was validated in a cohort of 56 blood samples from NF1 patients who fulfilled NIH diagnostic criteria, identifying the germline mutation in 53 cases (95% sensitivity). The efficiency and reliability of this approach facilitated detection of different types of mutations, including single-base substitutions, deletions or insertions of one to several nucleotides, microdeletions, and changes in intragenic copy number. Because mutational screening for minor lesions was performed using cDNA and the characterization of mutated alleles was performed at both the RNA and genomic DNA level, the analysis provided insight into the nature of the different mutations and their effect on NF1 mRNA splicing. After validation, we implemented the protocol as a routine test. Here we present the overall unbiased spectrum of NF1 mutations identified in 93 patients in a cohort of 105. The results indicate that this protocol is a powerful new tool for the molecular diagnosis of NF1. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.


Burkle L.A.,University of Washington | Burkle L.A.,Montana State University | Marlin J.C.,University of Illinois at Urbana - Champaign | Knight T.M.,University of Washington
Science | Year: 2013

Using historic data sets, we quantified the degree to which global change over 120 years disrupted plant-pollinator interactions in a temperate forest understory community in Illinois, USA. We found degradation of interaction network structure and function and extirpation of 50% of bee species. Network changes can be attributed to shifts in forb and bee phenologies resulting in temporal mismatches, nonrandom species extinctions, and loss of spatial co-occurrences between extant species in modified landscapes. Quantity and quality of pollination services have declined through time. The historic network showed flexibility in response to disturbance; however, our data suggest that networks will be less resilient to future changes.


Simons D.J.,University of Illinois at Urbana - Champaign
Perspectives on Psychological Science | Year: 2014

Trying to remember something now typically improves your ability to remember it later. However, after watching a video of a simulated bank robbery, participants who verbally described the robber were 25% worse at identifying the robber in a lineup than were participants who instead listed U.S. states and capitals—this has been termed the “verbal overshadowing” effect (Schooler & Engstler-Schooler, 1990). More recent studies suggested that this effect might be substantially smaller than first reported. Given uncertainty about the effect size, the influence of this finding in the memory literature, and its practical importance for police procedures, we conducted two collections of preregistered direct replications (RRR1 and RRR2) that differed only in the order of the description task and a filler task. In RRR1, when the description task immediately followed the robbery, participants who provided a description were 4% less likely to select the robber than were those in the control condition. In RRR2, when the description was delayed by 20 min, they were 16% less likely to select the robber. These findings reveal a robust verbal overshadowing effect that is strongly influenced by the relative timing of the tasks. The discussion considers further implications of these replications for our understanding of verbal overshadowing. © The Author(s) 2014


Johnson G.H.,University of Illinois at Urbana - Champaign | Fritsche K.,University of Missouri
Journal of the Academy of Nutrition and Dietetics | Year: 2012

The majority of evidence suggests that n-6 polyunsaturated fatty acids, including linoleic acid (LA), reduce the risk of cardiovascular disease as reflected by current dietary recommendations. However, concern has been expressed that a high intake of dietary n-6 polyunsaturated fatty acid contributes to excess chronic inflammation, primarily by prompting the synthesis of proinflammatory eicosanoids derived from arachidonic acid and/or inhibiting the synthesis of anti-inflammatory eicosanoids from eicosapentaenoic and/or docosahexaenoic acids. A systematic review of randomized controlled trials that permitted the assessment of dietary LA on biologic markers of chronic inflammation among healthy noninfant populations was conducted to examine this concern. A search of the English- and non-English-language literature using MEDLINE, the Cochrane Controlled Trials Register, and EMBASE was conducted to identify relevant articles. Fifteen studies (eight parallel and seven crossover) met inclusion criteria. None of the studies reported significant findings for a wide variety of inflammatory markers, including C-reactive protein, fibrinogen, plasminogen activator inhibitor type 1, cytokines, soluble vascular adhesion molecules, or tumor necrosis factor-α. The only significant outcome measures reported for higher LA intakes were greater excretion of prostaglandin E2 and lower excretion of 2,3-dinor-thromboxane B 2 in one study and higher excretion of tetranorprostanedioic acid in another. However, the authors of those studies both observed that these effects were not an indication of increased inflammation. We conclude that virtually no evidence is available from randomized, controlled intervention studies among healthy, noninfant human beings to show that addition of LA to the diet increases the concentration of inflammatory markers. © 2012 Academy of Nutrition and Dietetics.


Forbes M.M.,University of Illinois at Urbana - Champaign
The Journal of the Acoustical Society of America | Year: 2012

Sonoporation uses ultrasound, with the aid of ultrasound contrast agents (UCAs), to enhance cell permeabilization, thereby allowing delivery of therapeutic compounds noninvasively into specific target cells. The objective of this study was to determine if a computational model describing shear stress on a cell membrane due to microstreaming would successfully reflect sonoporation activity with respect to the peak rarefactional pressure. The theoretical models were compared to the sonoporation results from Chinese hamster ovary cells using Definity(®) at 0.9, 3.15, and 5.6 MHz and were found to accurately describe the maximum sonoporation activity, the pressure where a decrease in sonoporation activity occurs, and relative differences between maximum activity and the activity after that decrease. Therefore, the model supports the experimental findings that shear stress on cell membranes secondary to oscillating UCAs results in sonoporation.


Liu Y.T.,University of Illinois at Urbana - Champaign
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

Tidal torques acting on a gaseous accretion disk around a binary black hole can create a gap in the disk near the orbital radius. At late times, when the binary inspiral time scale due to gravitational wave emission becomes shorter than the viscous time scale in the disk, the binary decouples from the disk and eventually merges. Prior to decoupling the balance between tidal and viscous torques drives the disk to a quasistationary equilibrium state, perturbed slightly by small amplitude, spiral density waves emanating from the edges of the gap. We consider a black hole binary with a companion of smaller mass and construct a simple Newtonian model for a geometrically thin, Keplerian disk in the orbital plane of the binary. We solve the disk evolution equations in the steady state to determine the quasistationary, (orbit-averaged) surface density profile prior to decoupling. We use our solution, which is analytic up to simple quadratures, to compute the electromagnetic flux and approximate radiation spectrum during this epoch. A single nondimensional parameter g, equal to the ratio of the tidal to viscous torque at the orbital radius, determines the disk structure, including the surface density profile, the extent of the gap, the existence of an inner disk, and the accretion rate. The solution reduces to the Shakura-Sunyaev profile for a stationary accretion disk around a single black hole in the limit of small g. Our solution may be useful for choosing physical parameters and setting up quasistationary disk initial data for detailed numerical simulations that begin prior to decoupling and track the subsequent evolution of a black hole binary-disk system. © 2010 The American Physical Society.


Degnan P.H.,University of Illinois at Urbana - Champaign | Taga M.E.,University of California at Berkeley | Goodman A.L.,Yale University
Cell Metabolism | Year: 2014

The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities. © 2014 Elsevier Inc.


Kim D.H.,University of Illinois at Urbana - Champaign
Nature materials | Year: 2010

Electronics that are capable of intimate, non-invasive integration with the soft, curvilinear surfaces of biological tissues offer important opportunities for diagnosing and treating disease and for improving brain/machine interfaces. This article describes a material strategy for a type of bio-interfaced system that relies on ultrathin electronics supported by bioresorbable substrates of silk fibroin. Mounting such devices on tissue and then allowing the silk to dissolve and resorb initiates a spontaneous, conformal wrapping process driven by capillary forces at the biotic/abiotic interface. Specialized mesh designs and ultrathin forms for the electronics ensure minimal stresses on the tissue and highly conformal coverage, even for complex curvilinear surfaces, as confirmed by experimental and theoretical studies. In vivo, neural mapping experiments on feline animal models illustrate one mode of use for this class of technology. These concepts provide new capabilities for implantable and surgical devices.


Raine L.B.,University of Illinois at Urbana - Champaign
PloS one | Year: 2013

There is a growing trend of inactivity among children, which may not only result in poorer physical health, but also poorer cognitive health. Previous research has shown that lower fitness has been related to decreased cognitive function for tasks requiring perception, memory, and cognitive control as well as lower academic achievement. To investigate the relationship between aerobic fitness, learning, and memory on a task that involved remembering names and locations on a fictitious map. Different learning strategies and recall procedures were employed to better understand fitness effects on learning novel material. Forty-eight 9-10 year old children (n = 24 high fit; HF and n = 24 low fit; LF) performed a task requiring them to learn the names of specific regions on a map, under two learning conditions in which they only studied (SO) versus a condition in which they were tested during study (TS). The retention day occurred one day after initial learning and involved two different recall conditions: free recall and cued recall. There were no differences in performance at initial learning between higher fit and lower fit participants. However, during the retention session higher fit children outperformed lower fit children, particularly when the initial learning strategy involved relatively poor recall performance (i.e., study only versus test-study strategy). We interpret these novel data to suggest that fitness can boost learning and memory of children and that these fitness-associated performance benefits are largest in conditions in which initial learning is the most challenging. Such data have important implications for both educational practice and policy.


Lankau R.,University of Illinois at Urbana - Champaign
Biological Invasions | Year: 2010

Allelopathy has been increasingly invoked as a mechanism facilitating exotic plant invasions. However, studies even on the same target species often yield varying results concerning the strength and importance of allelopathic inhibition, suggesting that the process may depend on the specific environmental context. Here I studied how the allelopathic inhibition of sycamore (Platanus occidentalis) seedlings by garlic mustard (Alliaria petiolata) depended on the presence of a soil microbial community. Using three analytical approaches to quantifying allelopathy, I consistently found allelopathic inhibition only in sterilized soils, suggesting that certain microbial taxa inhibit the process, possibly by degrading the allelochemicals. Determining the environmental contexts that reduce or eliminate allelopathic inhibition could lead to a greater understanding of the spatial variation in invasion success and potentially lead to new avenues for management. © 2009 Springer Science+Business Media B.V.


Beymer-Farris B.A.,Furman University | Bassett T.J.,University of Illinois at Urbana - Champaign
Global Environmental Change | Year: 2012

Reduced Emissions from Deforestation and Degradation (REDD+) is being proclaimed as "a new direction in forest conservation" (Anglesen, 2009: 125). This financial incentives-based climate change mitigation strategy proposed by the UNEP, World Bank, GEF and environmental NGOs seeks to integrate forests into carbon sequestration schemes. Its proponents view REDD+ as part of an adaptive strategy to counter the effects of global climate change. This paper combines the theoretical approaches of market environmentalism and environmental narratives to examine the politics of environmental knowledge that are redefining socio-nature relations in the Rufiji Delta, Tanzania to make mangrove forests amenable to markets. Through a case study of a "REDD-readiness" climate change mitigation and adaptation project, we demonstrate how a shift in resource control and management from local to global actors builds upon narratives of environmental change (forest loss) that have little factual basis in environmental histories. We argue that the proponents of REDD+ (Tanzanian state, aid donors, environmental NGOs) underestimate the agency of forest-reliant communities who have played a major role in the making of the delta landscape and who will certainly resist the injustices they are facing as a result of this shift from community-based resource management to fortress conservation. © 2011 Elsevier Ltd.


Lankau R.A.,University of Illinois at Urbana - Champaign
New Phytologist | Year: 2011

Invaders can gain ecological advantages because of their evolutionary novelty, but little is known about how these novel advantages will change over time as the invader and invaded community evolve in response to each other. Invasive plants often gain such an advantage through alteration of soil microbial communities. In soil communities sampled from sites along a gradient of invasion history with Alliaria petiolata, microbial richness tended to decline, but the community's resistance to A. petiolata's effects generally increased with increasing history of invasion. However, sensitive microbial taxa appeared to recover in the two oldest sites, leading to an increase in richness, but consequent decrease in resistance. This may be because of evolutionary changes in the A. petiolata populations, which tend to reduce their investment to allelopathic compounds over time. These results show that, over time, microbial communities can develop resistance to an invasive plant but at the cost of lower richness. However, over longer time-scales evolution in the invasive species may allow for the recovery of soil microbial communities. © The Author (2010). Journal compilation © New Phytologist Trust (2010).


Tsai N.-P.,University of Illinois at Urbana - Champaign
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2014

The ubiquitin proteasome system is one of the principle mechanisms for the regulation of protein homeostasis in mammalian cells. In dynamic cellular structures such as neuronal synapses, ubiquitin proteasome system and protein translation provide an efficient way for cells to respond promptly to local stimulation and regulate neuroplasticity. The majority of research related to long-term plasticity has been focused on the postsynapses and has shown that ubiquitination and subsequent degradation of specific proteins are involved in various activity-dependent plasticity events. This review summarizes recent achievements in understanding ubiquitination of postsynaptic proteins and its impact on synapse plasticity and discusses the direction for advancing future research in the field. © 2014 Elsevier B.V.


Allison J.T.,University of Illinois at Urbana - Champaign
Engineering Optimization | Year: 2014

Rather than designing engineering systems from the ground up, engineers often redesign strategic portions of existing systems to accommodate emerging needs. In the redesign of mechatronic systems, engineers typically seek to meet the requirements of a new application via control redesign only, but this is often insufficient and physical system (plant) design changes must be explored. Here, an integrated approach is presented for the redesign of mechatronic systems involving partial plant redesign that avoids costly complete redesign. Candidate plant modifications are identified using sensitivity analysis, and then an optimization problem is solved that minimizes redesign cost while satisfying system requirements. This formal methodology for Plant-Limited Co-Design (PLCD) is demonstrated using a robotic manipulator design problem. The PLCD result costs significantly less than the full redesign, and parametric studies illustrate the tradeoff between redesign cost and performance. It is shown that the proposed sensitivity analysis results in the lowest cost limited redesign. © 2013 Taylor & Francis.


Chipot C.,University of Lorraine | Chipot C.,University of Illinois at Urbana - Champaign
Wiley Interdisciplinary Reviews: Computational Molecular Science | Year: 2014

In a matter of three decades, free-energy calculations have emerged as an indispensable tool to tackle deep biological questions that experiment alone has left unresolved. In spite of recent advances on the hardware front that have pushed back the limitations of brute-force molecular dynamics simulations, opening the way to time and size scales hitherto never attained, they represent a cogent alternative to access with unparalleled accuracy the thermodynamics and possibly the kinetics that underlie the complex processes of the cell machinery. From a pragmatic perspective, the present review draws a picture of how the field has been shaped and invigorated by milestone developments, application, and sometimes rediscovery of foundational principles laid down years ago to reach new frontiers in the exploration of intricate biological phenomena. Through a series of illustrative examples, distinguishing between alchemical and geometrical transformations, it discusses how far free-energy calculations have come, what are the current hurdles they have to overcome, and the challenges they are facing for tomorrow. © 2013 John Wiley & Sons, Ltd.


Denavit M.D.,University of Illinois at Urbana - Champaign | Hajjar J.F.,Northeastern University
Journal of Structural Engineering (United States) | Year: 2012

Accurate nonlinear formulations are necessary for the assessment of structures under seismic and other extreme loading. In this work, a three-dimensional distributed plasticity beam element formulation for circular concrete-filled steel tubes has been developed for nonlinear static and dynamic analyses of composite seismic force resisting systems. A mixed basis for the element formulation was adopted to allow for accurate modeling of both material and geometric nonlinearities. The formulation utilizes uniaxial cyclic constitutive models for the concrete core and steel tube that account for the salient features of each material, as well as the interaction between the two, including concrete confinement and local buckling of the steel tube. The accuracy of the formulation was verified against a wide variety of experimental results. The verification confirms the capability of the formulation to accurately produce realistic simulations of element and frame behavior. © 2012 American Society of Civil Engineers.


Winkler S.,University of Illinois at Urbana - Champaign
IEEE Journal on Selected Topics in Signal Processing | Year: 2012

Databases of images or videos annotated with subjective ratings constitute essential ground truth for training, testing, and benchmarking algorithms for objective quality assessment. More than two dozen such databases are now available in the public domain; they are presented and analyzed in this paper. We propose several criteria for quantitative comparisons of source content, test conditions, and subjective ratings, which are used as the basis for the ensuing analyses and discussion. This information will allow researchers to make more well-informed decisions about databases, and may also guide the creation of additional test material and the design of future experiments. © 2007-2012 IEEE.


Bavelier D.,University of Rochester | Green C.S.,University of Minnesota | Dye M.W.G.,University of Illinois at Urbana - Champaign
Neuron | Year: 2010

Children encounter technology constantly at home and in school. Television, DVDs, video games, the Internet, and smart phones all play a formative role in children's development. The term " technology" subsumes a large variety of somewhat independent items, and it is no surprise that current research indicates causes for both optimism and concern depending upon the content of the technology, the context in which the technology immerses the user, and the user's developmental stage. Furthermore, because the field is still in its infancy, results can be surprising: video games designed to be reasonably mindless result in widespread enhancements of various abilities, acting, we will argue, as exemplary learning tools. Counterintuitive outcomes like these, besides being practically relevant, challenge and eventually lead to refinement of theories concerning fundamental principles of brain plasticity and learning. © 2010 Elsevier Inc.


van der Donk W.A.,University of Illinois at Urbana - Champaign | Krebs C.,Pennsylvania State University | Bollinger Jr J.M.,Pennsylvania State University
Current Opinion in Structural Biology | Year: 2010

A growing number of non-heme-iron oxygenases and oxidases catalyze reactions for which the well-established mechanistic paradigm involving a single C-H-bond-cleaving intermediate of the Fe(IV)-oxo (ferryl) type [1•] is insufficient to explain the chemistry. It is becoming clear that, in several of these cases, Fe(III)-superoxide complexes formed by simple addition of O2 to the reduced [Fe(II)] cofactor initiate substrate oxidation by abstracting hydrogen [2,3•]. This substrate-oxidizing entry route into high-valent-iron intermediates makes possible an array of complex and elegant oxidation reactions without the consumption of valuable reducing equivalents. Examples of this novel mechanistic strategy are discussed with the goal of bringing forth unifying principles. © 2010 Elsevier Ltd.


Nikoobakht B.,U.S. National Institute of Standards and Technology | Li X.,University of Illinois at Urbana - Champaign
ACS Nano | Year: 2012

Inorganic nanomembranes, analogues to graphene, are expected to impact a wide range of device concepts including thin-film or flexible platforms. Size-dependent properties and high surface area-two key characteristics of zero- (0D) and one-dimensional (1D) nanocrystals-are still present in most nanomembranes, rendering their use more probable in practical applications. These advantages make nanomembranes strong contenders for outpacing 0D and 1D nanocrystals, which are often difficult to integrate into commercial device technologies. This Perspective highlights important progress made by Wang et al. (doi: 10.1021/nn2050906) in large-scale fabrication of free-standing nanomembranes by using a solution-based technique, as reported in this issue of ACS Nano. The simplicity of this new approach and the elimination of typical delamination processes used in top-down nanomembrane fabrications are among the strengths of this technique. Areas for improvement along with an overview of other related work are also discussed. © 2012 American Chemical Society.


Muturi E.J.,University of Illinois at Urbana - Champaign
Chemosphere | Year: 2013

The effects of anthropogenic chemical contaminants on aquatic organisms are largely influenced by underlying environmental conditions. This study evaluated how larval rearing temperature influences the impact of malathion on the fitness of the yellow fever mosquito Aedes aegypti. Larvae were exposed to water control, and low (0.03. mg/L) or high (0.05. mg/L) malathion dose at 20 °C, 25 °C and 30 °C and emergence rate, time to emergence, female fecundity and expression of genes encoding two antimicrobial peptides (defensin, cecropin) and an iron-binding protein (transferrin) quantified. High malathion dose at 25 °C and 30 °C resulted in significantly lower emergence rates compared to control and low malathion dose but this effect was not observed at 20 °C. Female time to emergence was inversely proportional to temperature and was significantly shorter in high malathion dose than in control and low malathion dose at 25 °C and 30 °C but not at 20 °C. Regardless of temperature treatment, females from high malathion dose were significantly larger and laid more eggs than their counterparts in control and low malathion dose. Relative to the controls, two immune genes were significantly over-expressed in adult females from malathion-exposed treatments at 20 °C (defensin and cecropin) and 25 °C (defensin and transferrin) and one gene (defensin) was significantly under-expressed at 30 °C. These findings suggest that larval rearing temperature can modify the effect of malathion on fitness traits in mosquitoes. © 2013 Elsevier Ltd.


Irwin S.H.,University of Illinois at Urbana - Champaign | Sanders D.R.,Southern Illinois University Carbondale
Energy Economics | Year: 2012

The 'Masters Hypothesis' is the claim that long-only index investment was a major driver of the 2007-2008 spike in commodity futures prices and energy futures prices in particular. Index position data compiled by the CFTC are carefully compared. In the energy markets, index position estimates based on agricultural markets are shown to contain considerable error relative to the CFTC's Index Investment Data (IID). Fama-MacBeth tests using the CFTC's quarterly IID find very little evidence that index positions influence returns or volatility in 19 commodity futures markets. Granger causality and long-horizon regression tests also show no causal links between daily returns or volatility in the crude oil and natural gas futures markets and the positions for two large energy exchange-traded index funds. Overall, the empirical results of this study offer no support for the Masters Hypothesis. © 2011.


Leggett A.J.,University of Illinois at Urbana - Champaign
Reports on Progress in Physics | Year: 2016

I present a brief review of the Landau Fermi-liquid theory of the normal and superfluid phases of liquid 3He, with emphasis on its philosophy, its successes and its limitations. © 2016 IOP Publishing Ltd.


Tse E.C.M.,University of Illinois at Urbana - Champaign
Nature Materials | Year: 2016

Many chemical and biological processes involve the transfer of both protons and electrons. The complex mechanistic details of these proton-coupled electron transfer (PCET) reactions require independent control of both electron and proton transfer. In this report, we make use of lipid-modified electrodes to modulate proton transport to a Cu-based catalyst that facilitates the O2 reduction reaction (ORR), a PCET process important in fuel cells and O2 reduction enzymes. By quantitatively controlling the kinetics of proton transport to the catalyst, we demonstrate that undesired side products such as H2O2 and O2 - arise from a mismatch between proton and electron transfer rates. Whereas fast proton kinetics induce H2O2 formation and sluggish proton flux produces O2 -, proton transfer rates commensurate with O–O bond breaking rates ensure that only the desired H2O product forms. This fundamental insight aids in the development of a comprehensive framework for understanding the ORR and PCET processes in general. © 2016 Nature Publishing Group


Orthopedic tissue engineering requires biomaterials with robust mechanics as well as adequate porosity and permeability to support cell motility, proliferation, and new extracellular matrix (ECM) synthesis. While collagen-glycosaminoglycan (CG) scaffolds have been developed for a range of tissue engineering applications, they exhibit poor mechanical properties. Building on previous work in our lab that described composite CG biomaterials containing a porous scaffold core and nonporous CG membrane shell inspired by mechanically efficient core-shell composites in nature, this study explores an approach to improve cellular infiltration and metabolic health within these core-shell composites. We use indentation analyses to demonstrate that CG membranes, while less permeable than porous CG scaffolds, show similar permeability to dense materials such as small intestine submucosa (SIS). We also describe a simple method to fabricate CG membranes with organized arrays of microscale perforations. We demonstrate that perforated membranes support improved tenocyte migration into CG scaffolds, and that migration is enhanced by platelet-derived growth factor BB-mediated chemotaxis. CG core-shell composites fabricated with perforated membranes display scaffold-membrane integration with significantly improved tensile properties compared to scaffolds without membrane shells. Finally, we show that perforated membrane-scaffold composites support sustained tenocyte metabolic activity as well as improved cell infiltration and reduced expression of hypoxia-inducible factor 1α compared to composites with nonperforated membranes. These results will guide the design of improved biomaterials for tendon repair that are mechanically competent while also supporting infiltration of exogenous cells and other extrinsic mediators of wound healing. Copyright © 2013 Wiley Periodicals, Inc.


Nitinawarat S.,University of Illinois at Urbana - Champaign
IEEE Transactions on Information Theory | Year: 2013

We study the capacity region CL of an arbitrarily varying multiple-access channel (AVMAC) for deterministic codes with decoding into a list of a fixed size L and for the average error probability criterion. Motivated by known results in the study of fixed size list decoding for a point-to-point arbitrarily varying channel, we define for every AVMAC whose capacity region for random codes has a nonempty interior, a nonnegative integer Ω called its symmetrizability. It is shown that for every L<Ω, CL has an empty interior, and for every L>(Ω+1)2, CL equals the nondegenerate capacity region of the AVMAC for random codes with a known single-letter characterization. For a binary AVMAC with a nondegenerate random code capacity region, it is shown that the symmetrizability is always finite. © 1963-2012 IEEE.


Dell G.S.,University of Illinois at Urbana - Champaign | Chang F.,University of Liverpool
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2014

This article introduces the P-chain, an emerging framework for theory in psycholinguistics that unifies research on comprehension, production and acquisition. The framework proposes that language processing involves incremental prediction, which is carried out by the production system. Prediction necessarily leads to prediction error, which drives learning, including both adaptive adjustment to the mature language processing system as well as language acquisition. To illustrate the P-chain, we review the Dual-path model of sentence production, a connectionist model that explains structural priming in production and a number of facts about language acquisition. The potential of this and related models for explaining acquired and developmental disorders of sentence production is discussed. © 2013 The Author(s) Published by the Royal Society. All rights reserved.


Branscomb E.,University of Illinois at Urbana - Champaign | Russell M.J.,Jet Propulsion Laboratory
Biochimica et Biophysica Acta - Bioenergetics | Year: 2013

The Submarine Hydrothermal Alkaline Spring Theory for the emergence of life holds that it is the ordered delivery of hydrogen and methane in alkaline hydrothermal solutions at a spontaneously precipitated inorganic osmotic and catalytic membrane to the carbon dioxide and other electron acceptors in the earliest acidulous cool ocean that, through these gradients, drove life into being. That such interactions between hydrothermal fuels and potential oxidants have so far not been accomplished in the lab is because some steps along the necessary metabolic pathways are endergonic and must therefore be driven by being coupled to thermodynamically larger exergonic processes. But coupling of this kind is far from automatic and it is not enough to merely sum the ΔGs of two supposedly coupled reactions and show their combined thermodynamic viability. An exergonic reaction will not drive an endergonic one unless 'forced' to do so by being tied to it mechanistically via an organized "engine" of "Free Energy Conversion" (FEC). Here we discuss the thermodynamics of FEC and advance proposals regarding the nature and roles of the FEC devices that could, in principle, have arisen spontaneously in the alkaline hydrothermal context and have forced the onset of a protometabolism. The key challenge is to divine what these initial engines of life were in physicochemical terms and as part of that, what structures provided the first "turnstile-like" mechanisms needed to couple the partner processes in free energy conversion; in particular to couple the dissipation of geochemically given gradients to, say, the reduction of CO2 to formate and the generation of a pyrophosphate disequilibrium. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. © 2012 Elsevier B.V.


Lankau R.A.,University of Illinois at Urbana - Champaign
Evolutionary Applications | Year: 2012

Invasive species can show substantial genetic variation in ecologically important traits, across ranges as well within the introduced range. If these traits affect competition with native species, then management may benefit from considering the genetic landscape of the invader. Across their introduced range, Alliaria petiolata populations vary in their investment in allelopathic traits according to invasion history, which could lead to gradients of impact on native species. Red oak (Quercus rubra) seedlings were transplanted into eight A. petiolata-invaded sites that varied in their invasion history and allelochemical concentrations. At each site, an invader removal treatment was crossed with experimental inoculations of native soil biota, to test whether the benefits of these restoration actions differed across invader populations. Q. rubra seedlings grew faster in invader populations with a longer invasion history and lower allelochemical concentrations. Invader removal and soil inoculation interacted to determine seedling growth, with the benefits of soil inoculation increasing in younger and more highly allelopathic invader populations. A greenhouse experiment using soils collected from experimentally inoculated field plots found similar patterns. These results suggest that the impact of this invader varies across landscapes and that knowledge of this variation could improve the efficacy and efficiency of restoration activities. © 2011 Blackwell Publishing Ltd.


Cimpian A.,University of Illinois at Urbana - Champaign | Leslie S.-J.,Princeton University
Science | Year: 2015

Ginther and Kahn claim that academics' beliefs about the importance of brilliance do not predict gender gaps in Ph.D. attainment beyond mathematics and verbal test scores. However, Ginther and Kahn's analyses are problematic, exhibiting more than 100 times the recommended collinearity thresholds. Multiple analyses that avoid this problem suggest that academics' beliefs are in fact uniquely predictive of gender gaps across academia. Copyright 2015 by the American Association for the Advancement of Science.


Dorgan V.E.,University of Illinois at Urbana - Champaign
Nano letters | Year: 2013

We study the intrinsic transport properties of suspended graphene devices at high fields (≥1 V/μm) and high temperatures (≥1000 K). Across 15 samples, we find peak (average) saturation velocity of 3.6 × 10(7) cm/s (1.7 × 10(7) cm/s) and peak (average) thermal conductivity of 530 W m(-1) K(-1) (310 W m(-1) K(-1)) at 1000 K. The saturation velocity is 2-4 times and the thermal conductivity 10-17 times greater than in silicon at such elevated temperatures. However, the thermal conductivity shows a steeper decrease at high temperature than in graphite, consistent with stronger effects of second-order three-phonon scattering. Our analysis of sample-to-sample variation suggests the behavior of "cleaner" devices most closely approaches the intrinsic high-field properties of graphene. This study reveals key features of charge and heat flow in graphene up to device breakdown at ~2230 K in vacuum, highlighting remaining unknowns under extreme operating conditions.


Belmont A.S.,University of Illinois at Urbana - Champaign
Current Opinion in Cell Biology | Year: 2014

Traditionally large-scale chromatin structure has been studied by microscopic approaches, providing direct spatial information but limited sequence context. In contrast, newer 3C (chromosome capture conformation) methods provide rich sequence context but uncertain spatial context. Recent demonstration of large, topologically linked DNA domains, hundreds to thousands of kb in size, may now link 3C data to actual chromosome physical structures, as visualized directly by microscopic methods. Yet, new data suggesting that 3C may measure cytological rather than molecular proximity prompts a renewed focus on understanding the origin of 3C interactions and dissecting the biological significance of long-range genomic interactions. © 2013 Elsevier Ltd.


Jo Y.,University of Illinois at Urbana - Champaign
Economics and Human Biology | Year: 2014

This paper investigates the relationship between family income and childhood obesity. Using the Early Childhood Longitudinal Study, Kindergarten Class of 1998-99 (ECLS-K), I report three new findings. First, family income and childhood obesity are generally negatively correlated, but for children in very low-income families, they are positively correlated. Second, the negative association between family income and Body Mass Index (BMI) is especially strong and significant among high-BMI children. Third, the difference in obesity rates between children from low- and high-income families increases as children age. This study further investigates potential factors that might contribute to a rapid increase in the obesity rate among low-income children. I find that their faster weight gain, rather than slower height growth, is a greater contributor to the rapid increase in their BMI over time. On the other hand, I also find that the faster weight gain by low-income children cannot be attributed to any single factor, such as participation in school meal programs, parental characteristics, or individual characteristics. These findings add to the current obesity debate by demonstrating that the key to curbing childhood obesity may lie in factors generating different obesity rates across income levels. ©2014 Elsevier B.V. All rights reserved.


Klein M.V.,University of Illinois at Urbana - Champaign
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

In 1966, Leggett used a two-band superconductor to show that a new collective mode could exist at low temperatures, corresponding to a counterflow of the superconducting condensates in each band. Here, the theory of electronic Raman scattering in a superconductor by Klein and Dierker (1984) is extended to a multiband superconductor. Raman scattering creates particle/hole (p/h) pairs. In the relevant A1g symmetry, the attraction that produces pairing necessarily couples excitations of superconducting pairs to these p/h excitations. In the Appendix, it is shown that for zero wave-vector transfer q, this coupling modifies the Raman response and makes the long-range Coulomb correction null. The two-band result is applied to MgB2 where this coupling activates Leggett's collective mode. His simple limiting case is obtained when the interband attractive potential is decreased to a value well below that given by local-density approximation (LDA) theory. The peak from Leggett's mode is studied as the potential is increased through the theoretical value. With realistic MgB2 parameters, the peak broadens through decay into the continuum above the smaller (π band) superconducting gap. Finite q effects are also taken into account, yielding a Raman peak that agrees well in energy with the experimental result by Blumberg [Phys. Rev. Lett. 99, 227002 (2007)]10.1103/PhysRevLett.99.227002. This approach is also applied to the q=0, two-band model of the Fe pnictides considered by Chubukov [Phys. Rev. B 79, 220501(R) (2009)]10.1103/PhysRevB.79.220501. © 2010 The American Physical Society.


Havlicek J.,University of Illinois at Urbana - Champaign
Child Maltreatment | Year: 2014

Little is known about maltreatment among foster youth transitioning to adulthood. Multiple entries into out-of-home care and unsuccessful attempts at reunification may nevertheless reflect extended exposure to chronic maltreatment and multiple types of victimization. This study used administrative data from the Illinois Department of Children and Family Services to identify all unduplicated allegations of maltreatment in a cohort of 801 foster youth transitioning to adulthood in the state of Illinois. A latent variable modeling approach generated profiles of maltreatment based on substantiated and unsubstantiated reports of maltreatment taken from state administrative data. Four indicators of maltreatment were included in the latent class analysis: multiple types of maltreatment, predominant type of maltreatment, chronicity, and number of different perpetrators. The analysis identified four subpopulations of foster youth in relation to maltreatment. Study findings highlight the heterogeneity of maltreatment in the lives of foster youth transitioning to adulthood and draw attention to a need to raise awareness among service providers to screen for chronic maltreatment and multiple types of victimization. © The Author(s) 2014.


Salje E.K.H.,University of Cambridge | Dahmen K.A.,University of Illinois at Urbana - Champaign
Annual Review of Condensed Matter Physics | Year: 2014

Recent experimental and theoretical progress on the study of crackling noise in the plastic deformation of crystals, ferroelastics, and porous materials is reviewed. We specifically point out opportunities and potential pitfalls in this approach to the study of the nonequilibrium dynamics of disordered materials. Direct optical observation of domain boundary movement under stress and experimental results from acoustic emission and heat-flux measurements lead to power-law scaling of the jerk distribution with energy exponents between 1.3 and 2.3. The collapse of porous materials under stress leads to exceptionally large intervals of power-law scaling (seven decades). Applications in geology and materials sciences are discussed. © Copyright 2014 by Annual Reviews. All rights reserved.


Gadway B.,University of Illinois at Urbana - Champaign
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2015

We present a simple experimental scheme, based on standard atom-optics techniques, to design highly versatile model systems for the study of single-particle quantum transport phenomena. The scheme is based on a discrete set of free-particle momentum states that are coupled via momentum-changing two-photon Bragg transitions, driven by pairs of interfering laser beams. In the effective lattice models that are accessible, this scheme allows for single-site detection, as well as site-resolved and dynamical control over all system parameters. We discuss two possible implementations, based on state-preserving Bragg transitions and on state-changing Raman transitions, which, respectively, allow for the study of nearly arbitrary single-particle Abelian U(1) and non-Abelian U(2) lattice models. © 2015 American Physical Society.


Mayerich D.,University of Illinois at Urbana - Champaign
BMC bioinformatics | Year: 2013

Vibrational spectroscopic imaging is now used in several fields to acquire molecular information from microscopically heterogeneous systems. Recent advances have led to promising applications in tissue analysis for cancer research, where chemical information can be used to identify cell types and disease. However, recorded spectra are affected by the morphology of the tissue sample, making identification of chemical structures difficult. Extracting features that can be used to classify tissue is a cumbersome manual process which limits this technology from wide applicability. In this paper, we describe a method for interactive data mining of spectral features using GPU-based manipulation of the spectral distribution. This allows researchers to quickly identify chemical features corresponding to cell type. These features are then applied to tissue samples in order to visualize the chemical composition of the tissue without the use of chemical stains.


Kumar P.,University of Illinois at Urbana - Champaign
Water Resources Research | Year: 2011

Prediction problems broadly deal with ascertaining the fate of fluctuations or instabilities through the dynamical system being modeled. Predictability is a measure of our ability to provide knowledge about events that have not yet transpired or phenomena that may be hitherto unobserved or unrecognized. The challenges associated with these two problems, that is, forecasting a future event and identifying a novel phenomenon, are distinctly different. Whereas the prediction of novel phenomena seeks to explore all possible logical space of a model's behavioral response, the prediction of future events seeks to constrain the model response to a specific trajectory of the known history to achieve the least uncertainty for the forecast. Predictability challenges have been categorized as initial value, boundary value, and parameter estimation problems. Here I discuss two additional types of challenges arising from the dynamic changes in the spatial complexity driven by evolving connectivity patterns during an event and cross-scale interactions in time and space. These latter two are critical elements in the context of human and climate-driven changes in the hydrologic cycle as they lead to structural change-induced new connectivity and cross-scale interaction patterns that have no historical precedence. To advance the science of prediction under environmental and human-induced changes, the critical issues lie in developing models that address these challenges and that are supported by suitable observational systems and diagnostic tools to enable adequate detection and attribution of model errors. Copyright 2011 by the American Geophysical Union.


Freyfogle E.T.,University of Illinois at Urbana - Champaign
Harvard Environmental Law Review | Year: 2010

Private property and liberty, particularly in the case of privately owned land, are intertwined more complexly than we commonly realize. When we study how private property operates in daily life, looking at the full array of land-use conflicts, what we see is that private rights backed by state power are as apt to restrict liberty as they are to promote it. To understand the multiple, contradictory ways that property is linked to liberty is to see why we cannot start with the idea of liberty, or with any conception of natural rights, and produce from it a working, morally justified system of private property. To produce such a system, we need to start instead in a much different place, looking to the various ways that private property can foster the common good. Ultimately, lawmakers crafting and updating a scheme of private property must choose among the many types of liberty that they want to secure, based on their assessment of the common good. Only after they have done that, choosing among the options and paying attention to overall social utility, can we see how private property promotes liberty. These observations have considerable relevance to the ways we think and talk about property, land-use regulations, and takings jurisprudence.


Gille Z.,University of Illinois at Urbana - Champaign
Environment and Planning A | Year: 2010

The author argues for the necessity of a macro-theoretical framework for a systematic understanding of the waste-society relationship-a synthesis of the Marxist mode of production concept and the posthumanist concept of actor networks, sociomaterial assemblages, or collectives. Based on empirical data on Hungary's socialist and capitalist waste history (1948 to the present), it is shown that macro dynamics are qualitatively different from micro ones and thus their analytical separation is retained. At the same time, it is demonstrated that the common fallacy of Marxist and posthumanist theories to conflate social scale with level of abstraction unduly demonized macro-level concepts. Finally it is shown that existing syntheses of Marxism and actor-network theory cannot but treat waste as a theoretical derivative of the concept of value, and thus elide waste's concrete materiality. The concept of waste regime is proposed to resolve these shortcomings. © 2010 Pion Ltd and its Licensors.


Lankau R.A.,University of Illinois at Urbana - Champaign
Oecologia | Year: 2011

Invasive species can benefit from altered species interactions in their new range, and by interfering with species interactions among native competitors. Since exotic invasions are generally studied at the species level, relatively little is known about intraspecific variation in the traits that determine an invader's effect on native species. Alliaria petiolata is a widespread and aggressive invader of forest understories that succeeds in part by interfering with mutualistic interactions between native plants and soil fungi. Here, I show that the impact of A. petiolata on soil microbial communities varied among individuals due to variation in their allelochemical concentrations. The differential impacts translated into varied effects on native tree growth, partly because A. petiolata's allelochemicals preferentially affected the most mutualistic fungal taxa. These results highlight the importance of considering the spatial and temporal variation in an invasive species' impacts for understanding and managing the invasion process. © 2010 Springer-Verlag.


Freund J.B.,University of Illinois at Urbana - Champaign
Physics of Fluids | Year: 2013

Small slits between endothelial cells in the spleen are perhaps the smallest blood passages in the body, and red blood cells must deform significantly to pass through them. These slits have been posited to participate in the removal of senescent blood cells from the circulation, a key function of the spleen. One of the effects of red blood cell aging is an increased cytosol viscosity; relaxation time measurements suggest their interior viscosity can increase by up to a factor of 10 toward the end of their normal 120 day circulating lifetime. We employ a boundary integral model to simulate red blood cells as they deform sufficiently to flow through such a small passage, whether in the spleen or in a microfluidic device. Different flow rates and cytosol viscosities show three distinct behaviors. (1) For sufficiently slow flow, the pressure gradient is insufficient to overcome elastic resistance and the cell becomes jammed. (2) For faster flow, the cell passes the slit, though more slowly for higher cytosol viscosity. This can be hypothesized to facilitate recognition of senescent cells. (3) A surprising behavior is observed for high elastic capillary numbers, due either to high velocity or high cytosol viscosity. In this case, the cells infold within the slit, with a finger of low-viscosity plasma pushing deeply into the cell from its upstream side. Such infolding might provide an additional mechanism for jamming, and the sharpness of the resulting features would be expected to promote cell degradation. Linear analysis of a model system shows a similar instability, which is analyzed in regard to the cell flow. This linear analysis also suggests a similar instability for unphysiologically low cytosol viscosity. Simulations confirm that a similar infolding also occurs in this case, which intriguingly suggests that normal cytosol viscosities are in a range that is protective against such deformations. © 2013 AIP Publishing LLC.


Caetano-Anolles G.,University of Illinois at Urbana - Champaign
Journal of Molecular Evolution | Year: 2015

Phylogenetic reconstruction of ribosomal history suggests that the ribonucleoprotein complex originated in structures supporting RNA decoding and ribosomal mechanics. A recent study of accretion of ancestral expansion segments of rRNA, however, contends that the large subunit of the ribosome originated in its peptidyl transferase center (PTC). Here I re-analyze the rRNA insertion data that supports this claim. Analysis of a crucial three-way junction connecting the long-helical coaxial branch that supports the PTC to the L1 stalk and its translocation functions reveals an incorrect branch-to-trunk insertion assignment that is in conflict with the PTC-centered accretion model. Instead, the insertion supports the ancestral origin of translocation. Similarly, an insertion linking a terminal coaxial trunk that holds the L7–12 stalk and its GTPase center to a seven-way junction of the molecule again questions the early origin of the PTC. Unwarranted assumptions, dismissals of conflicting data, structural insertion ambiguities, and lack of phylogenetic information compromise the construction of an unequivocal insertion-based model of macromolecular accretion. Results prompt integration of phylogenetic and structure-based models to address RNA junction growth and evolutionary constraints acting on ribosomal structure. © 2015, Springer Science+Business Media New York.